I'm pretty new to eQuest, and have only used it for simple simulations up to this point. Right now I'm trying to model a pretty large building with multi-level roofs. Once I get to the shells that model the top floors of my building, I have to change the footprint shape. Think of modeling a winner's podium, where positions 1, 2, and 3 all end at different heights. However, when I remove sections from the footprint, eQuest repositions my shell. I think it's trying to center it on top of the lower floors rather than let me put it where I'd specified.

When making new shells, I've been choosing to position them immediately above the preceding floor. I then trace over the shape of the last floor in the custom footprint, making any necessary changes. I've messed with specifying the exact site coordinates, but that hasn't helped. 

Sorry if I didn't do a great job explaining my problem - the attached images may help.