amsdenj

The horn has a couple of purposes. First its to provide dispersion of your guitar tone so that more than just the few people that are right in front of it and right on axis get the high end. Second is to provide full range flat frequency response for other patches that say include acoustic guitar or mic inputs. 
 
Now to the high cut on cab and IR models. Although an electric guitar pickups don’t produce much above 6 kHz, and guitar speakers often reproduce even less, a distorted guitar with a mic pointed right at the speaker cone can result in substantially higher frequencies than that. Hence the fizz. This is not unusual for mic’d analog amps and cabinets. Microphone choice and placement are a real art for capturing a good electric guitar sound. And it usually takes some post EQ, compression, limiting, etc. in the recorded track to get what we’re use to hearing. Live this stuff doesn’t matter as much because its LOUD. But in headphones, or with monitor speakers at normal room volumes, it will matter a great deal. This is why you need to use high cut on Helix cab and IR blocks - to reproduce the whole signal chain.
 

They're all a bit different, not necessarily better or worse. HD500 lost some things X3 had, and gained some others. I generally thought the HD500 sounded better on most things than the X3. But there are still some tones on the old POD 2.0 that are worthwhile and hard to reproduce on anything else. That said, I'm happy with Helix and am glad to have less hardware choices.

To use Helix with Logic, you should consider first recording dry inputs for your mic and guitar. That way you can re-amp with Helix or other plugins like S-Gear or Bias FX. By default the direct guitar is set to USB 7 and the direct mic USB 8. You can change these in global settings if needed to select specific Helix inputs. Note that USB 7/8 can't be selected in a Helix Output Block, its dedicated to dry outputs for re-amping purposes.
 
I think your problem is the outputs. Unless you need to specifically send outputs to Logic tracks outputs to specific USB inputs routed to Helix effects sends and returns, you should set the output of each Logic track to the Stereo output, then configure Mac OS and Logic to use USB 1/2 for the Stereo output - this should be the default. Helix dedicates USB input 1/2 to output from your computer, it can't be selected as an input in an Input Block, bypasses all block processing and is always active. You should now be able to play audio from your computer to USB 1/2 and hear it in the Helix headphone jack.
 
Now we can address the inputs. You have a couple of choices. If you have your Helix output blocks set to Multi, then you will hear your processed guitar and mic signals directly from the Helix headphone output, with no latency. And USB 1/2 can be selected as inputs to a stereo track in Logic. In this case you want input monitoring off in Logic since you are already monitoring direct from Helix. This will work, but it will record the guitar and mic stereo signals into the same stereo track, so all the mixing would need to be done in Helix and can't be changed in Logic. Generally this isn't what you want, unless you want to record essentially a live performance from Helix to see exactly what your audience would hear using the same configuration.
 
If you want to separate the guitar and mic into two stereo tracks, then you need to set the Helix output block of the guitar path to USB 3/4 and the output block of the mic path to USB 5/6. Note you can also use USB 1/2 for either the guitar or mic, but not USB 7/8, these are dedicated to dry signals. But this will only direct monitor one of your instruments, so it should be avoided. Then select the appropriate USB inputs in the Logic tracks for the guitar and mic signals.
 
At this point you will not be able to monitor your guitar and mic from the Helix headphone output because the Helix Output blocks are set to USB 3/4 and 5/6 and so they aren't sending any output to the headphones. You can use global settings to change what the the headphones monitor: Multi (including 1/4", XLR and USB 1/2), 1/4" outputs, or XLR outputs. You want to leave it on Multi so you can monitor USB 1/2 which is the output of your computer.
 
To monitor the tracks, all you need to do is turn input monitoring on in the Logic tracks. Latency shouldn't be a problem if you have a reasonably recent Mac computer with a reasonably recent OS. If it is, open the Logic audio preferences and reduce the buffers on the audio device. Do this until you get some digital noise and then increase the buffers a bit.
 
At this point you should be ready to go. 
 
Note that Logic Pro X has been available for a few years and is quite an improvement in every way over the version you have as shown in your screen shot. The prices is also very reasonable. You might want to consider an update.

1. Yes, you can use a mix block in front of the looper to mix to mono. However anything that is input to the looper is summed to mono if the looper is set to mono. In your case, you're already mixing two things, so you already have the mix block.
 
2. Although a looper overdub is stored in separate memory (in order to support one-level Undo), this has no impact on the memory required for multiple overdubs. The memory used is established by the first recording, which establishes the loop length. All other overdubs are simply mixed with this content. 
 
3. The looper has no stop and fade out mode, but you could simulate that with an expression pedal controller on the looper playback level parameter.
 
You might find the blog posting helpful: Using a Looper for Solo Gigs

I found it, its the preset numbering option in the Global Display settings. Forgot where it was.

I did some experimenting tonight and found that the Flip Top bass amp with no cabinet model is the flattest amp, and works reasonably well with a Variax 700 acoustic. Its a little darker than with no amp, but pretty transparent with the tone controls set at 50%. The voicings probably aren't great for acoustic guitar since its a bass amp. But I do recall that Ampeg bass amps used hi-fi boost/cut tone controls, not the all boost controls used by Fender. This is an option to explore until version 2.6 comes out.

I found the answer in the advance manual of all places. The foot switches do respond to received MIDI, but on specific CC numbers, not the ones you configure in the MIDI control page. All I need to do is change all the MIDI mappings in MainStage to use the default CC messages assigned to the foot switches, then I think it will work. Will try that tonight.
 
The more I dig into and use the POD HD500X, the more I like it.