The way I put together a piece of music and IK stuff is wholly incompatible. When I am laying out the structure of a song, I tend to break it up into 8/16 or whatever bars. I then set record mode to loop and track until i get the take right. IK's Ampeg thing and Amplitube do not handle looping at all.
I can get a sound I like while Sonar is paused, then disable SVX. I can then apply the effect afterwards.
That method sux in that I cannot play the amp. This is more of an issue to me with the guitar sims, where I like to dig into the strings and hear the dynamics and harmonics show back up in the sim.
If you track non-stop start to end, this will not be an issue.
For me, I have active electronics on my bass and can get a wide range of tones going direct. I run it through the front of my UA LA610 so I have a tube pre in the chain.
I can get sounds I like from Revalver and Guitar Rig, though sometimes just putting a limiter on it to even it out is enough for me. I really prefer the direct bass sound for all but the most thunderous of moments.