I'm not sure, but I think the original form was "assied", and "assois" is just some kind of common usage that was used so much it had to be accepted.
Anyway, both are good. We mostly use the "assois" form here in Canada : maybe it's much different in France. I don't know. For us, someone that says "je m'assieds" either didn't learn french in Quebec, or tries to give himself some pompous style of speaking. In either cases, it sounds a bit weird.
We do conjugate it commonly using the imperative form, as in "Assied-toi !", "Sit down !".