What parts/areas of the SEs should be supported in an HSC?
In my experience you don't have to worry nearly as much about supporting specific areas of the guitar as you do with a Les Paul since the body and neck angle are flat on a PRS. I'd say, as long as the body is laying flat you should be fine. Also, make sure the neck isn't being supported by the headstock since there's more headstock angle than on a Fender, for example. I have fender cases that fit my PRS perfectly, but the tip of the headstock is too low, so it keeps the neck from laying flat.