Hope you've got it by fixed by now, if not:
Right click on the jpg you placed (hopefully you not did not place it directly on the layout), in the "Drawing Selection Settings" > Properties > Pen set , look for the check box "transparent background", check it. If it is grayed out , then the jpg version you are using is not supported by AC.
If transparent background is grayed out: use Display Order. Set the Site Display Order to "send to back". Then it will not cover anything up. However your building drawing view will now be transparently over the Site, so you'll want to make sure to control the plan view's layers and drawing extents. If need be, create cover fills to control building transparency.
Snap