I've got my fair share of fat, and the "on top" position has been confusing for me ... it's something my boyfriend has had to be patient with as I "learned how" to do it. [It's a long distance relationship, so we don't get to have a lot of sex.]
I do feel a little self-conscious about my tummy, but otherwise it's just something I have had to "feel out" ... what feels good to me, what feels good to him ... like Caroline said, clitoris stimulation is a great plus to this position!
If you lift your hips up a bit, he can thrust with you on top, too, and I don't know if it's the angle on me or what, but that's one of my favourite positions