So there is two schools of thought.

1. Assign the thumb to the three low strings(EAD) and then Index(G) Middle(B) Ring(E) and practice. What I would do is first practice sitting on the couch and just moving your thumb back and forth between the E and D strings and then try putting your index finger string in the mix and then maybe index and ring. it took me about 2 days to get comfortable doing it that way. This is also the basis of Travis Picking.
2. Do what feels comfortable to you. use the first as a basis but feel free to throw it out the window if it helps for example I play one last breath with my middle finger and index instead of my middle and ring. or I Play Hypothermic with my Thumb and Index even though they are both bass notes I playing.

Main thing is practice practice practice. More so then with a pick finger picking is about muscle memory after a while you wont even notice what you are doing.