You can put the FX block anywhere really I just put it in front or after the noise gate if I'm using one so it acts more like a boost pedal driving the amp a bit more but if you were on a really clean patch and wanted to keep it clean I suppose you could put it at the end as well.  You're correct after that assign it to a footswitch and you can assign other effects as well.  Set your patch to the default you want i.e. on off of various effects and hit save then it will turn things on and off with the click of one switch.

I love my HD more and more.  I was enjoying dialing in the tones for each song for each worship service and have gotten quite good at it.  I've posted many of them to Customtone.  Search Worship.  Anyway, through all my experimenting I've come up with one tone now that I have used for all songs for the past 2 months.  I will post it next time I have my HD hooked up to my computer.  Really the only tweak I've had to do is modify the delay slightly.  With the upgraded models, the DEP's it really is very responsive, cleans up really well with the volume control on the guitar turned to about 80% and has just enough dirt at 100%.   We play the current P&W stuff you hear on K-LOVE nothing really heavy like Skillet so it's perfect.

I do have a JTV and all I can say is save up your nickels and birthday money because it is well worth it!  When I was creating individual song patches I'd also save my Variax settings as well so that it was switching my guitars sounds too.  We've gone all wireless at our church so now I just switch them manually, plus with this patch I'd have to anyway.  I find myself using mostly the R-Billy pos 2 (Gretch Duo-Jet Bridge), Semi-5 (ES-335 Neck), and Spank-5 (Strat Neck).  I have also used the acoustic on occasion though we usually have a dedicated acoustic guitar player.  I have used the on-the-fly tuning changes alot as well.  We'll have a vocalists that at rehearsal decide they can't do it in the original key and it save a lot of time recharting and relearning songs and fingerings.

One of best improvements for the Variax came with the 2.0 release for the HD.  It was the ability to change and store the tunings on the unit itself.  It was quite the PITA to store alternate tunings in your HD patches before and the instructions were not exactly crystal clear.  I had to do it about 10 times before I finally figured it out and I did it so irregularly that I'd have to relearn it each time.  Now I can do it right on the HD unit and it's done.

I've used the unit direct out and since January through at DT-50 to a 1x12 Blackheart cabinet mic'd with an SM-57.  I recently just switched to a DT-25 head and used that for the first time this past weekend.  I really liked this combo the best.  I heard the playback and was really pleased not that the DT-50 sounded bad, it didn't it's just that I think I can get more tube saturation with the DT-25.  If you're interested you can hear/see this past week's service at www.covechurch.org  go to watch this week.  It may be under the message tab like 2nd from the left on the top.  You'll see the rig, hear the worship tone I spoke of and best of all see me! LOL  I'm the only electric this week so if you hear electric it's the "rig!"