So after doing more research I changed the design a bit.
Filter sock will go straight into the 45. There will be a baffle in the 45 seperating the "fuge" area from the "sump" area. I'll place the skimmer, heaters and sock in the sump area. From there, water will flow into the fuge area (rock rubble and frags).. the drain will be in the fuge area, draining into the 35g. (not sure if I should add a sock in here as well)..
Chaeto will be in the middle chamber.. Return chamber will also have my media reactor pump which will feed the frag section on the 45g.