Functionally, it doesn't matter. It works either way. I have mine on the bottom, rear. AJ had his mounted that way and got some pretty nasty rubbing. One thing that would possibly help would be to move the SB brackets out a smidge with 1/8" spacer. More clearance may help.
If they are mounted with the resevoir on the bottom, it will move with the swingarm. If it contacts the bags, since it is moving up and down, it could damage the bags. If it is mounted up top, it may hit the bags, but it isn't moving up and down and any damage would be significantly less. Plus, spacing the bags out at the top would benefit the top mounted resevoir most.

Thanks again for all the pointers in this thread. I mounted mine with the reservoirs up and toward the front of the bike. No problems at all with clearance on the right bag, but it was pretty close on the left one. If i pushed on the inside of the bag, I could get it to hit the reservoir. So, I tweaked the forward saddlebag bracket a bit, which helped and then put the fuzzy side of a piece of velcro on the bag just in case. Should be good to go! Packed my spanner wrench and looking forward to seeing how the bike behaves vs. the Progressive 440s that were on there before on the trip to/at/from MV next week.