that's kind of what i figured you were going for.
Here's my suggestion for doing this:
Have both pipes from the bulkheads connect into a wye (with a valve right at the bulkhead for the skimmer section) and then you can pump both sections down at once just by opening the skimmer section valve when you do your water changes. This would require you to also have the return pumps discharge piping valved and tee'd off so you can divert the flow to the sink... But that would make water changes fast and easy for sure!
that is exactly what is planned!!!!!!