My setup uses inside the boot pants that fit over my jumbo knee protectors. Keeping mud and dirt out of the knee protectors keeps them moving freely, and I don't have to clean them. A pocket or two would be nice but I keep all of my pocket stuff in an Ogio vest which also carries a water bladder.
Over the boot pants seem to be more common for on road riding where keeping rain water out of your boots would be important. I haven't flood my boots yet crossing a river but at that point, over-boot or in-boot pants probably don't matter much.
'03 KTM 450EXC
"If you know what you're doing, then you aren't learning anything." - A. Lincoln