This has probably been eluded to here and there, but I just wanted to point it out explicitly because it just bit me again...
If you use multiple processes, the gcode from the 1st process is the one that controls the print.
However, there is other gcode inserted by other processes based on tool change and temperature settings etc.
So.. if you have a 2nd process based on the first process, and you don't want it to change your temperature settings HINT HINT S3D (I really hope they fix those temperature bugs in the next release....), you might want to remove the temperature controllers from your 2nd and subsequent processes.
Glad I printed a small test print or I might have ruined a 13 hour print I'm about to start after 12.6 hours since I used a different process for the last few mm.
Sheesh...