The only time I use amp sims is for tracking DIs for later reamping with real amps, but I've had decent results applying EQ to the DI signal before the amp sim. It takes some pretty drastic EQ changes in order to cause a negligible difference in the sound you hear after the amp sim, though. When I tracked all the rhythms for my band's album I used Pod Farm, and basically just dialed in the absolute best sound I could using only parameters and options within Pod Farm (tubescreamer, amp settings, post EQ, cab/mic...everything), and then ended up still scooping out a good chunk of low end/low mid and crap on the DI before the amp sim. It's probably best viewed as a last resort, and if you intend to actually reamp later, definitely don't print your EQ to the DI files, just leave them raw. In my case, the DIs sounded just fine and ready for real amps, but the EQing I did was necessitated by the fact that the small version of Pod Farm I have (I didn't buy the more expensive one) doesn't have a huge amount of tone options...