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One efficient way to do it that will save an FX Block is to use the Channel Volumes of each amp model as an  Expression Parameter. What you need to do is note the percentage value of each channel volume, remove the button assignment and turn on both amps...Assign the Channel volume of each amp to the Expression and assign like the example below...Basically, just invert the MIN and MAX between them and they will crossfade pretty decently...You can add an Expression pedal to dedicate this...
 
AMP A: Channel Volume Set to 85%
AMP B: Channel Volume Set to 70%
 
Expression parameters like this:
 
    AMP B Channel Vol. MIN = 0%
    AMP B Channel Vol. MAX = 70%
   
    AMP A Channel Vol. MIN = 85%
    AMP A Channel Vol. MAX = 0%

The 1/4 outs are unbalanced...

use the aux input or set the guitar input impedance to 3M and use that one...make sure you set the second input to Variax or Mic so you don't get the level increase....top input would be guitar or aux depending on which you want to use...the impedance changes the tone, so hogher is better, but it can be used to adjust for something being overly bright....usually better when the guitar hits it....think strat or tele....
 
use a 1/4 main out back to the fx loop return...use line level...input settings is on page 3 or 4 in the system menu...

That is most curious. Usually this can mean the preamp in the Boogie might not be biased right or something is going one there. Usually, putting an active buffer between your guitar and amp will solve this. But you have the problem with the active buffer in line....This can be indicative of a cable problem some place where you have ground leakage in to places that loop back...Does it do it with other guitars also? Try different cables and different guitars if you can...

The trim pot is plastic, so a lot of things can work. I use a little plastic flathead with one hand and my other hand is behind my back.  ;)

An HD500 or HD500x is nearly EXACTLY the same as the HD Desktop in terms of available settings. The only real difference is the lack of the Line 6 link and midi. The HD400 is like the the Spider IV and Spider Valve modeling preamps in terms of setting and options....Different animal then the HD500, HD Pro and HD Desktop....Only models themselves are the same.
 
The HD500X is a minor hardware revision from the HD500 and has slightly more DSP.

make sure that your interface does NOT have echo turned on. This is interface specific. Old Edirol USB-> midi interfaces were notorious for having echo on by default and cause countless issues back in the old Flextone III and Vetta II days. A little app like midiOX might help sort that out.

This looks to be a pretty decent article on that. Even goes into the caps and pots with a nice diagram.
 
http://www.singlecoil.com/docs/paula.pdf

I have the FBV Shortboard (MK2 also)....It works great with my HD Bean...Should not be any different with a HD Pro X...One thing to check is the pedal calibration....The reflector sometimes bends slightly with wear to the point it won't calibrate correctly....I have had to straighten mine once in 10 years....still works great and the display kills the MK2....

I am guessing that you have the L2M hooked up via the link....USB playback will not go over the link (I have a couple of DT amps that have the link)...rather, you would likely need to run the 1/4 outs out of the 500x to the RCA inputs on the L2M to get soundcard playback with you guitar...

B has two outputs...So what you want is an 8 ohm cab if you want to use it with your internal speaker...
 
So yes, you can move the internal speaker from the 8 ohm out to one of the 4 ohm outs...plug your 8 ohm cab in the other and you should be good to go...

There is no magic setting for leveling the relative volume of patches....No other way than setting the master and leaving it, then going thru the patches and adjusting the channel volume only...

I have old EMU 1820 interface and HD Desktop works just fine with that....My interface has 8 analog inputs and I have recorded my HD Desktop using unbalanced cables and balanced cables (L and R ourputs are TRS)....My interface also has a coax spdif IO also....that works fine too for recording the POD...You can take a dry input off the spdif in the POD at the same time you take the processed on the Analog outs if you setup the pOD that way...If you interface supports ASIO configuration, then re-amping the dry track isn't much of a problem at all...It's just configuring the pathc IO on your interface...

Power....The DT50 does Fender spank tone better than the DT25....But that is to be expected as you need power to do a twin tone with the right dynamics...DT25 doesn't do that very well at gig volume....DT50 does....I have both amps...rehearse with the DT25, gig with the DT50....DT25 is underpowered playing alongside a real drum kit...At least it is for me...

Yes, assuming you are using the AMP Model in the HD500....It needs only to be enabled....When the AMP Model in the HD500 is disabled and you are on Channel B, then everything in the HD500 is before the DT50 on the system link...IOW, the Line 6 System Link is one-way...

Yes, the Class, Mode and NFL all affect the power amp configuration and response. The Class and Mode are pretty straight forward. Class A Pentode is probably the most transparent to a certain point of pushing the power amp...Once you push it to a certain point the bottom end is going to get spongy...Class AB will give more transient spank and punch (dynamics) than Class A will...triode mode will darken the repsonse a bit and reduce power...So that likely is not the way you want to go...but those combinations are easy to try...jsut flip the switches...If you mean clean headroom like a Twin, then I would say try Class AB Pentode...If you want it to breathe a little, try Class A...either way can be pretty darn clean...really depends on how loud you are running and your own taste...and the tricky part...
 
The tricky part: Depending on what pre models you have loaded in the NFL selector changes the Negative Feedback Loop which affects the power amp response pretty drastically based on the selected NFL (or model)...The control not only select the preamp model, it will also change how hard the buffer hits the power amp and the Negative Feedback circuit, which will affect clean headroom pretty dramatically...How this happens is technically a little bit different between the DT25 and DT50 but the results as nearly the same. I would say the place to start is loading the amp with some amp models you like...spin up some tones that are close to what you are looking for and snap a few photos of how you have it set so it is easy to remember...Then switch over to your preamp and see what works...

A couple of things you need to try I think...
 
You need to turn the "Bypass Volume" to 0 on each amp model....You can only set this when the amp model is disabled....Once you do this, you will likely need to rebalance the channel vol when the amp is enabled...
 
One suggestion I have is that you try using the PRE versions of the amp models you are using...Since you have a nice tube power amp a FULL model is kinda overkill IMHO and you get a bit more DSP for other things too...

I have a Flextone III XL and use it with my HD Desktop for rehearsals....The tones I use are setup for using DT50, DT25, SVs....I generally use two amps...One set Class A and an SV (AB)...My patches are certainly not optimized for the Flexy as I use PRE models...However, for rehearsals I change the POD to Combo Front and cut a good amount of 400-600 hz and it translates pretty well to what the tube amps sound like...I am thinking that I will probably close off the back of the Flexy as that is the real problem with that amp...the back is way too open...Still a great amp...

Is that a question? Seems you have a preconceived notion....
 
Conventional guitar amplifiers do not have tweeters...The are not full range....The full range notion is when cab and mic modeling....That is the sound of a mic on an amp....If that is your game you need to get a POD and a keyboard amp or something like that....SV is a guitar amp bro...loaded with a V30....It's a combo amp....It's class AB tube power amp with a digital preamp on the front....The preamp is modeled...The XLR out is full range...Again, it's a guitar amp...

right...the combo gets half the power and the cab gets the other half...where the combo speaker gets around 12 watts, each speakers in the cab is seeing around 4-5 watts...
 
You would likely get a bit better cone volume match if you changed the combo to a 16 ohm speaker...parallel combined load with your 8 ohm cab is about 5.3 ohms...no problem on the 4 ohm tap. I have been running my SV MK1, MK2, DT50 and DT25 with a 5.3 ohm load for years...however, I do it but using a 212 cab loaded with 16 ohm speakers...all my 112 combos have 16 ohm speakers...Three 16 ohm speakers in parallel is 5.3 ohms...cone volume is balanced...In your case, a 16 ohm speaker with an SPL rating that is -3db less than Vintage 30s would likely get pretty close...