Tough question. If using the JTV stand alone, you are sort of "stuck". Whatever pickup position you select for models is also the one used for the mags. You can move around where models are stored using workbench and try to line up common combinations better.
If using a POD with VDI, you can lock the model and pickup switch so that if you change position of pickup switch only the magnetic pickups are effected.
An example. I use duncan prails on my JTVs to get more tonal variations. On a typical country patch I use tele bridge on the model side and the p rail set to single coil for mags. Two different single coil sounds into two different amps with one amp delayed 20ms gives a great and wide sound.
I use the POD HD to force the bridge pickup on the tele and lock the pickup selector in HD edit. So now if I switch to neck position on the pcik up selector the mags switch to say the p rail on p90 but the models stay on tele bridge. Sort of sounds like a tele with p90 in neck but with stereo jack. neck pickup to one amp and bridge to another. Pretty darn cool actually.
The problem is if I want to have both mags and models switch to neck, I need a different patch to be set to not lock pickup selector.
I would LOVE the ability to send the apropriate midi PC message to change variax models to the variax via VDI from the POD. I could assign an IA switch on the FBV to be tele neck. That way on a patch where the pcikup selector is locked I can still get two options.
Just moving selector to neck will get me that cool "stereo" sound where neck goes to one amp and bridge to another. However if I move selector to neck and stomp on the IA they both switch to neck position. Heck I would get a third option where I keep the mags on bridge and stomp the IA to get neck pickup on tele for similar stereo effect but swapped as to which amp gets models and mags.
If Line 6 allowed changing just variax "patch" via IA on a POD things would get much cooler. Use an IA to stay in same patch but just change tuning for slide etc.
Change actual guitars via IA switch. Lets say in my example above with tele on bridge and p rail single coil bridge for mags. Use that for the main parts of a tune but for the solo I want a different sound. Switch mags to neck p90 and stomp that IA to switch to a custom model I made in workbench of a 355 with mini humbucker in the neck.