Sounds like our pools are plumbed in similar fashion.
I have a valve that controls the suction feed into the pump, the two inputs on the valve are from the skimmer and from the main drain at the bottom of the pool. I can close off the skimmer port to get 100% feed from the pool bottom's main drain, or close off the main drain to get 100% flow through the skimmer...or have it set anywhere in between with partial flow from both.
For normal operations I leave the valve in the middle...with both ports wide open.
When I vacuum through the skimmer box, I find that I the vac can float off the pool floor with the valve in that middle position, so I close off the bottom drain a bit to get more flow through the skimmer. I rotate the valve just until I can hear the pump straining a bit, it makes using the vacuum much more effective.
If I were to close off the bottom drain completely and go 100% skimmer, the suction is so strong and the overall flow through the vacuum hose is so restricted that the pump really labors. It pulls so hard that it actually "shrinks" the length of my vacuum hose by several feet, and the hose becomes too short to reach the far end of the pool!
So there's a happy medium in there for me. You'll find one for yours too.