I'm guessing the sound will be the same either way.
Try both and see what works best for you. I would definitely have each guitar going to it's own amp sim and not doubled up.
As far as what plugs to use....there are no rules. I use the so called mastering stuff on my tracks when I think that's the sound I want.
Stacking the FX in different orders will change the sound results so again... play around and see what sounds best to you.
I use busses with the FX in them when I have say... several vocal tracks or several guitar tracks and want the same reverb on all of them.... a buss is very handy for that. PLUS.... by putting the verb and compression or whatever in a buss, the track is still clean (no FX) so if I want to try a specific FX I can effect only that one track and this is really handy when running melodyne to fix a vocal track.
nope...FF is broken when it concerns this forum. I use chrome.