I use CT, and manual trim. Manual trim for when your aircraft gets below about 150 ish or when you get far too fast. Most of the time i have CT on.
Auto-speed, i leave at the default settings (which should be at or close to best sustained climb for your aircraft). I use it for auto-climb to climb out after taking off. I also use it if i need to glide some distance with a dead engine.
Auto-angle, is usefull for holding a set up/down attitude - like diving, or zooming.
Auto-level, i use for cruising straight and level.