You can use cheats to teleport armies next to their cities (although the Roman naming-system may be hard to understand).
If other mods are mod-foldered as EB is, in theory everything should work fine. The inclusion of mini-mods can increase the chance of getting failures in the game, but it doesn't have to.
Regarding CTD's: Open a thread here with as most information as you can give, in the most times there can be something done.

XSamatan