I do something similar - a thin thin change pad that was left over from my cloth diapering days (it's a layer of PUL and a layer of thin fleece), and on top of that a thin hemp or cotton prefold. I make sure to wrap the edge of the water proof part up the back a bit, and to also wrap it up between the crotch strap and the child. I've made the mistake of not doing that, and also made the mistake of no absorbent layer, and both resulted in the pee just pooling and running out the edge. Properly positioned though it works nicely.
There's no official answer to what is the right way to do it. The 'right way' is never pee in your car seat
Sitting on what is basically a diaper, that until very recently they were wearing, doesn't concern me. It's not thick, it's not interfering with harness fit or adjustment, and common sense must prevail. No one likes cleaning a stinky pee car seat.