So I can now choose A and B correctly, but I don't understand when to use which order.
Glad you're starting to like the method, and glad that it is starting to make more sense! It does seem like a lot at first, but trust me. Over time it becomes second nature to see which commutator you need for any given cycle.
As for choosing which direction, whether to use an ABA'B' commutator or a BAB'A' commutator, it all depends on the "lone piece" and which piece the A part of the commutator replaces in the B part slice turn.
Here is a cycle:
(URB RFD ULF)
Here I see that the interchangeability is on the U face. I can interchange URB and ULF with the turn U2. This means that I must insert the RFD corner into the U layer affecting either the ULF or the URB corner, but nothing else in the U layer.
I will do this by A = L D' L'
Now I need to see where the RFD corner needs to go to, and compare this to which spot the A part of my commutator places it. The RFD corner, the lone corner, needs to go to ULF. The A part of the commutator places the RFD corner at ULF. This means that where I need the corner to go from my cycle, and where the A part of my commutator places the RFD corner both line up at the ULF spot. This means I will do an ABA'B' commutator.
Now say I had the cycle (URB ULF RFD)
Here I see that the URB and ULF corners are interchangeable by a U2 turn. I also see that I can insert the lone corner, the RFD corner, into the U layer by A = L D' L'
Now I compare where I want the RFD corner to go with where the A part of my commutator sends it to. I want the RFD corner to go to URB, but the A part of my commutator places it at ULF. These do not line up, therefore I am going to interchange with the B part of my commutator first. I am going to do the turn U2 first, and thus do a BAB'A' commutator.
Whether you do ABA'B' or BAB'A' depends only on where you want to lone piece to go compared to where the A part of the commutator places it.
Hope that helps,
Chris