You most likely need one amp sim per guitar track - unless those two guitars never play at the same time. Amp sims should be used as track insert, on each individual guitar track. Bussing and sending multiple tracks to the same amp isn't really an option if you want good results. Unless you're after some experimental sonic mayhem.
Though there are no rules, but if you're using a tube booster, it's likely that you should put it before the amp.
To avoid CPU issues, freezing would be the best option.