I like pictures as they can show me details!
Your overall drain system and these pictures are snips from this parts info:
cortona.winnebago.com
At the small tank, when you want to drain it?
You need to open this valve to let waste go to pump Before starting pump as running dry is not good for pump! Open this valve before or after opening valve at large tank would seem to make no difference? At some point both need to be open before turning pump on! No big deal if pump is on first but it can't move much with either valve closed!
Open small valve at main tank, some may move gravity flow but turn on pump to move the rest?
I would do this , get all waste from small out and rinse if doing that, then turn off pump, close both valves and be done with the small tank. Nothing says both have to be drained at same time but I tend to do both whie at the job?
then after that question is out of the way, I do the larger tanks, black first and grey second. Theory says grey last to flush but in your case there is not a lot of black to flush except in the drain hose.
Two small valves and pump to drain small. one large handle on each black and grey main tanks to drain them. Close all when done??? Don't run pump long when totally dry to avoid wear on it!