I've been helping a neighbor friend build a two-level workbench with mortice/tenon joinery. We used my Powermatic morticing machine to cut the (large) mortices, and then a combination of table saw and bandsaw to cut the tenons. We cut the shoulders of the tenons on the TS, using a stop block to establish the distance of the cut from the ends of the boards. For shorter pieces, we then used my old Delta tenoning jig on the TS to make the cheek cuts. For longer pieces, we used his bandsaw.
The trick is to keep the "reference surface" in mind when doing the cuts. That is, the surface from which all measurements are based.