Welcome to the forum.
I'm puzzled by your statement about hardly any water in the skimmer. Do you mean the pump basket? In any case, bubbles in the return jets indicates a suction side leak. If you mean the pump basket empties overnight then you could have a leaks between the various ports of a multi-port valve if you have one. What type of filter? A common sneak path with these valves is to the waste line. You may be getting s dribble out there and when you turn off the pump air can get sucked in and drain the pump basket. A valuable piuece of info is the actual amount of water you're losing. Put a piece of tape on the skimmer or measure water depth to some known reference. Knowing the approximate surface area of the pool you can then calculate the gallone per hour you're losing.
Al