I finally got this issue sorted out. Here's how:

I ran wargus in a virtual machine via VirtualBox with the CD mounted through there. After running it, I copied the following to /media/mmc1/games/stratagus, which already contained the UI elements for the N900 screen:

1. The contents of the 'data' directory'
2. All contents of the wargus directory, using the 'Merge' option.

tarek : )