I would make the skimmer section as tall as possible while having the skimmer on a stand and still able to pull out (enough head room) because the returm will be the same if not lower then this section.
From what i've heard about filter socks they are ok to run for a short peroid of time to clean up the water. But they tend to clog fast and hold materail that the skimmer would pull out. I think some you can tie to the input to the sump. So you should be able to tie one on when needed if the pipe is high enough off the LR rubble in the bubble tower.