A picture isn't going to help, really. There are too many variables going on to be able to say, "set the collection cup XX inches above the skimmer body". Each tank will be different. And even then, you will have to move it up and down depending on what's going on in the tank.
With my Remora, right now, I have the cup almost all the way down. That's because the tank is fairly free of dissolved organics, but I'm still trying to recover from a little tank melt down a couple weeks ago. So I'm wanting to skim really wet. But other weeks, for whatever reason, the thing will fill up within an hour at that setting... so I raise the cup up during those times.
The Remora is about as plug-and-play as you get for a skimmer - no airline tubes to clog up or clean, and even if the collection box fills up and wants to overflow it just drains back into the skimmer and not all over your floor. But you do have to keep an eye on how wet the skimmate is, and raise or lower the collection box accordingly. And in your situation, it sounds like it needs lowering.