The Nissan Path

I got my pathfinder with 2 remotes. One factory and one aftermarket.
I found out that with the OEM one I can roll my windows down automagically, but not back up.

With the aftermarket one, I can roll them up, but not down.

What is the OEM behaviour supposed to be? Is there supposed to be an auto roll up/down?

OEM is down only, just like most all other cars these days. Why not up? Something something consumer liability.

Aftermarkets can do just about anything and I would guess they will roll down too if you can figure out how to program it.

So, considering that I apparently already have a module in the car for auto-up, is there a way to program the OEM key fob? The aftermarket one is garbage!

Highly doubtful. The modules usually run separate, although I've seen some systems able to reprogram the OEM remote to work with it. Need to research the aftermarket system and find someone that knows how it works.