How about if at the end of a turn on the province info screen the guerilla activities was listed with a loss in money attached that would be rectified by increasing troops or happiness? Maybe have some units lose a few men, similar to how an uprising caused this previously?
The other option is an ambush where the rebels attack but then disappear quickly, rather than running round and round till you pin them down. Would follow the info we have where AI decides wether to weaken you or fight to the finish and would have a morale penalty on your men. Would accurately portray how annoying the guerillas were to regular troops.
On the topic of how effective they were, in the Penninsula war I think it was documented that the guerillas accounted for more deaths than regular troops and didn't they make a French army surrender at Bayers?
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