I think its in the rulebook somewhere, but I don't have it with me.
The reason why there are different numbers of Invader markers is due to the circumstances of the Invaders. The Eastern invader is usually the one faced with the stiffest resistance from the USA and hence captures less area's than the Western invader. The Western invader, once he gets past the coastal cities, is faced with less opposition untill he reaches the Rocky Mountains where Partisan cards can stop him. Thus, the Western invader usually captures more territory than the Eastern Invader and thus needs more markers.
But in the end, if you run out you can just use other markers (like coins) or remove them from area's where you already have infantry (so that its clear who the area belongs to). As I said before, the only limited things in this game are the units and the Partisan/Invader cards, where there are specific rules as to what to do when you run out or there are strict limits on how many you should have available at the start of the game.