Not 100% sure how it works exactly, but don't worry about it, if it works how it is. I think it always starts with front left and then goeas in a specific order.
I have a quad system with 4 output channels, and it goes FL, FR, SL, SR, starting from output channel analog 1 for front left (to 4 for surround right). If i had some other speakers on my outputs 1 and 2, i could set MA1 to start from 3 and counting up to output 6, because in that case i don't want it to use outputs 1 and 2.
With RME Totalmix, "output channels" can be routed to different hardware outputs, though. In my case i still chose Analog Output 1 in MA1 although my front speakers are actually connected to SPDIF. But in TotalMix, Analog 1 output channel is routed to the FL SPDIF hardware output.