Ok, I literally just bypassed Kontakt in logic, I routed my drums to separate outs in kontakt, routed those to separate stereo buses in logic, then to audio tracks with the buses as inputs, tadaa printed drums. I then Alt-clicked Kontakt as the input of the software instrument track in the mix window to bypass it. I now have multi tracked drums and a bypassed plug?
Remember in Logic 9 you could open a new project and through it's browser, import tracks+plugins+settings from an existing project into it, so you always have them to go back to. Then bounce in place and remove kontact from the other, freeing cpu. if you then later make changes, just bounce and import them back using the same process.
Explaining the problem a bit more thoroughly would've helped. I thought you were having issues doing the actual bounce!
Create arranger track literally creates an arrangement track that is linked to the mixer object you created it for - allowing for automation and the like for multi-outs or busses or something similar.