Blocks and some settings within blocks (Hi-Res IRs, High quality reverbs, etc) increase the CPU percentage. You want to keep the CPU percentage below 80%. After 80%, the FM3 will give a "Warning". If it greatly exceeds 80%, the audio from the FM3 shuts off.
Many applications. Check out page 27
of the FM3 manual.
What are you trying to do exactly? Record and play through an amp at the same time? I think reading through Section 4/page 27 of the manual will help you out.