Well as for the skimmer, put it down in the sump! You are right it's not pretty to look at. The main reason for a sump is to as you said get the heaters and stuff out of the main tank but it also serves another purpose and that is adding more water volume to your system.
To really get the benefits of a Fuge it needs to have a little size to it. In your case you have a 46bow and probably not a lot of room under the tank. A 20g long tank divided up could work well for you. I took my system a step further and I have a 20gtall tank that is a dedicated fuge. I have a 10g return sump and a 15g acrylic sump that is getting ready to be tied to the system for even more water volume.
Adding a fuge with LR LR
rubble and Macro Algae will greatly improve your water quality. Doing regular PWCs will keep it that way!