We anchor stern in all the time, both in our current boat and in our previous Sea Ray. No trick to it, except you need to be mindful of how much water is there vs how much you need to keep your drive from hitting bottom when the tide goes out. I do it either of two ways, depending on the spot:
Set the bow anchor as usual, either by hand or windlass (love that thing!), then if water is warm and I'm getting in anyway, I wade my spare anchor in toward the beach (or even on the beach in some places) and set it, then tie off to the aft cleat and pull boat around till she is stern in to the beach. I usually walk around by the outdrive while we are anchored up this way and kind of judge my depth at various times to make sure the tide isn't going out too fast. If I need the boat to be out a little farther, I let some line out on the stern anchor and take some in from the bow. If you set your bow anchor a little farther out than you plan on being, you will have some extra scope to work with as the tides change.
The second variation of this is just that I just throw the stern anchor out a ways if I'm not getting in and then use the stern cleat to pull the stern around to the desired position and tie off.
When leaving, if you are in doubt as to whether or not you have enough water under the drive to motor out, you can always haul in the stern anchor and pull yourself out toward the bow anchor, which should put you in deeper water.
Also...If you are in a busy area with lots of boats and swimmers, its not a bad idea to mark your anchors with a small buoy or flag to keep folks from tripping or stumping a toe if they walk by your anchor. I actually had a guy try to take my stern anchor because his kids saw it on the beach and told him they found an anchor just lying there...he didn't get far and once he put two and two together he was really embarrassed

...we thought it was hilarious because we watched the whole operation from the boat, wondering what they were doing with my anchor...you run into all kinds of "special" peeps on the water, I guess.
Anyway...that's what works pretty well for us. Good luck!