i am sorry i am still confused on the holes. i must be wasting oxygen tonight.

it sounds like there are 4 holes total in the back of the tank, correct? if this is the case and you are thinking of having 2 pumps for the CL system then you would not need a SCWD. there will not be any thing to switch between. 1 hole for inlet and 1 for outlet on the CL.
ohhh, are you thinking of these holes as returns and not closed loops? i think my brain may have just turned on.

you will now be returned to your regularly scheduled program. got it now, i think.
all of these holes are on the back glass, so they will be behind the rockwork, which is good. this is the hardest place to get detritus out of. i do not think that switching the current around back there will help that much. i would think making 2 of the holes as a spray bar back low behind the LR to try and push the detritus out. you could then use the other two for general circulation throughout the tank. run some hidden PVC up near the top of the rockwork.
i am planning on having over 3500gph in my 125g by the end of the year. the more flow the better. if you are using the 4 holes for returns then you will run into problems keeping bubbles out of your display due to the skimmer. you will be trying to push insane water through your sump. generally ends in bubbles.
sorry, i will try and edit this tomorrow. my brain turned off again.

to much info for me to delete, and i am not writing anything in a usefull manner. i have either thoroughly confused you, and/or got you rethinking your setup.
G~