Your joints will still meet square and your tenons will still be perpendicular to those surfaces. You may have to offset or alter the tenons depth, but that should be all, unless you have a radical design in mind. Do a prototype, keep your design simple until you get the knack of it. Don't over think the problem, most people do and they give up before they even try. I still draw new design full size to work out the bugs, plus it helps with angles and templates when you finalize a design.
