Make the large-scale magic effects integrate with the base rules. Spells could result in eg:
+1 or -1 on attacks or saving rolls
+ or – on move distances
negate or enhance terrain effects
Different armies (fantasy races or whatever) could have access to different kinds of spell in keeping with their character.
The magical commander(s) might have an absolute fixed number of specified spells at the start; or a set number of Power points to spend on spells as they wish; or Power might fluctuate according to time passed, or friends/enemies slain, or magical locations captured, etc etc etc.