You should really download the medmod. It greatly balances the game and fixes some issues as well as letting you play some factions that aren't available in the regular game.
Being execommunicated means that the Christian factions might launch crusades on you which could be very bad. If your Emperor is old then you should go for a land grab amongst the Christian lands as once he dies the excommunication is rendered void.
You should uncheck the option that tidies up units after battles. It makes it easier to remember which unit is where, which army is which as the game seems to mess that up badly. (click the little gray rectangle right beside the mini map to see those options).
Keeping track of who to move where.. keep your army units tight and units that are guarding provinces in the castles so they don't clutter the map up.
Having a fleet is useful only against warring factions and to maintain naval superiority in a given sea area.
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