I have kept Flame Angels and currently have a Coral Beauty Angel. They can be aggressive to similarly-shaped newcomers, but I haven't had either bother corals.
you could put him in the large tank and be prepared to catch and move him to the smaller tank if he comes under attack, or put it in the smaller tank up front.
As a side note, a 5 foot tank doesn't seem appropriate for an adult emperor angelfish, unless we're talking about an oddly sized tank like a cube with lots of swimming area...