I have my game set to start a mode on the plunge, so my steps are below.
1) start a mode and finish it (while ball save is on...open orb and lock first ball)...I don't do Quill's because points are much bigger after a few modes are completed. I don't do Kyln, as I only start that when a multiball is one shot away.
2) while not in a mode, get Groot to final lock ready (any time the orb is open from a random hit...lock the second ball).
3) before locking third ball in Groot (or orb if it's open and ready) shoot the scoop and start a mode.
4) start Groot MB and finish it and the current mode
5) orb should be ready for third lock by now (if not get it ready)...start new mode and then start orb
6) finish orb and current mode
7) rinse, repeat with Groot, orb and modes. Try not to be in one without another.
8) if you're getting close to II, just qualify last few modes instead of trying to finish them.
This is obviously harder said than done, but it's my basic strategy. I get deep into the game on a regular basis using this. The game will let you qualify modes and time them out for safety, but where is the fun in that. I've often finished everything and started II and SX back to back.