Some thoughts: Why the chaeto and not a dsb?
I suspect the first baffle is way too high. Personally i would lower it, to ensure more water reaches the first compartment. With reduced flow to improve skimmer efficiency, you will sacrifice the liverocks efficiency as a filter. (possibly becoming a nutrient trap) You will be amazed at how much crap is missed by a skimmer, and this will settle into the pores of your liverock. Maybe adding some pumps in there would help.
Personally I would remove the liverock and use the chamber as a settlement area, then do liverock followed by a dsb or chaeto.
Also, if drilling is an option, I would have the skimmer chamber overflow drilled and directed towards the beginning of the first bottom chamber.