The thread you are thinking of is here:
http://forum.arcadecontrols.com/index.php?topic=37448.msg333628#msg333628In your case, it is not a question of rewiring, since your X axis is still your X axis, and your Y axis is still your Y axis. According to u_rebelscum, what you would need to do is run your XD and YD leads through an inverter chip. (This is a chip that makes a low signal into a high, and a high into a low) See u_rebelscum's post in the above thread for the details.
My inverter chips just arrived yesterday, and I have already soldered together a small interface board for the chip. I'm planning on installing and testing the chip this weekend. I'm in the same boat as you--things are remapped in Mame, but they're pretty funky elsewhere. (Actually, even within Mame after remapping things aren't perfect--i.e. in the config menus for instance)
I will report back here with the results and possibly photos of the setup.. stay tuned!
-88mph