The easiest solution is to have 2 copies of W:A installed in different folders -- one with PX installed (using 3.6.31.0) and the other copy with the newest patch (3.7.2.1).
I recommend to have 2 copies of W:A installed, instead of just using the PX version for everything, because there are some minor bugs in PX that will occasionally cause desynchronization (game-ending) errors while playing non-PX games. There are also some other bugfixes not related to PX in the newer version.
Also there is worse support for multi-monitors in 3.6.31.0 (wkD3d9wnd doesn't work in the older version). The multi-monitor support is really nice and slick using wkD3d9wnd, so this is a pretty big deal for me.
Please note that you need a non-Steam version of W:A to use ProjectX --- you can only install the older patch on a non-Steam version of the game. So you need to acquire the CD version or an unmodified ".ISO" file.... from a legal source of course