Have all different types of food, dont take in enemy nation troops and vist taverns to increase morale. I have 400+ never hit desertion lvls.

Investing in leadership will slightly help, but I find having a baggage train is the best option as it provides 60 morale. You can get one either by exchanging 2 'various loot' items to any tavern keeper, or paying 500 coins to a steward of a castle/town you own, but you can only have one at a time. Get loot from bandit and hateful enemies like jatu and mystmountain (chance depending on loot skill) and hidden chests in rane and valonbray. Also, speaking to your castle/town steward, you can organise a feast which provides twice the morale than a tavern does.

If you are getting your baggage trains from your towns/castles it doesn't limit you to only one. You can get another one from each of your towns/castles each week or so. I had loads of them with no problems.