I haven't personally done rocks over the geotextile, but know some guys that have put rocks straight onto clay. The rocks always managed to sink into the clay and disappear over time. Therefore, I think you will definitely have better results using the fabric below the rock.

As regards other advice, I think your rocks will tend to move downslope even when they are on the fabric. I have read (on Pond Boss?) that a good solution is to build a lip in your fabric and rocks to stop or retard this movement.

Hopefully, some of the good plant guys can help you on your other questions.

Good luck on your project!