Placement and Size of Coralife Protein Skimmer

I have almost completed my tank transition, moving my old 55 gallon setup with the Aqueon sump with my new 93 gallon rimless cube. Along the way, I discovered that my Aqueon sump would not fit into my tank stand. Total error on my part! So I went to the LFS and purchased a repurposed 20 gallon tank with baffles to serve as my new sump. However, now I have an issue on the placement of my Coralife skimmer. When hanging on the sump (20 gallon tank), the skimmer collection lid sits too high, and will not fit. Is my only option placing the skimmer in the sump, rather than hanging on the side? Is this a reliable setup? Are there any other options? (Smaller cups, displaced cups, etc).