First of all I have to thank the authors of this fantastic mod which has given to me a whole new game experience and which I personally consider more as a new game rather than a mod.
Therefore I hate "having issues" but I cannot resist the temtation to suggest a possible minor improvement in terms of historical accuracy and hopefully gaming experience as well.

It is cool that the EB Team tried to implement logistics into the game, but IMO the armies should not be penalized for moving on the enemy territory and resupplied by staying there (pillage), but vice versa.
I base my objection on various historical sources, namely Xenofon´s Anabasis. His Ten Thousand were quite happy while marching through hostile lands as they could take whatever they liked and actually enrich themselves. On contrary many problems arised when they entered friendly greek colonies on the Black Sea shore, because now the have to buy their provisions. Also it was common during prolonged sieges that the besieging army pillaged the nearby country and subsquently run out of provisions sooner than the besieged and the siege had to be abandoned.
Therefore I suggest that:
1.- General moving on enemy territory (i.e. he has less than 50% movement points left at the end of turn) should gain a trait "raiding" or "booty", giving him some cash income (say 1000 mnai). This would represent the historical army living off enemy land and decreasing its upkeep costs as the provisions are taken from the enemy.
2.- The supply traits already used (rationing, etc.) should be invoked while the army is "pillaging" (represented in the game by those black spots). This would represent the unavailability of food on the territory already plundered.
3.- (This would probably could be done only for provinces with a family member in town as a governor, but role-players mostly have one and if the AI would not be that affected by this it won´t mind) The governor of a province which has enemy army on its soil should gain a trait like "enemy raid" or so, causing 50% decrease of tax income and 50% derease of trade income. This would represent the severe impact of an enemy invasion to the province.

I am looking forward to your comments on this idea. Sorry for the long post.