Well you didn't describe much a a vast trading empire so my usual answer to this won't apply. You obviously just have too many armies vs. the amount of income. Stupid answer but that IS the answer.

Solution? Cash raising expedition. If you are losing money every turn you cannot wait around. It won't change magically on its own. If you cannot afford to build farms and trade posts you MUST do something ASAP.
ATTACK and pillage
Look around you. Anyone in a rich province you think you can woop real quick?
Go attack...take the pillage money...then walk back to your home without taking the castle. Yes he'll take the province back. But you just pillaged 1000 or 1500 florins. Do this as you see fit and able. Use the cash to build farms and traders and ships.

One thing I think players fail to realize at first but learn later is you make SOOOOOO much money with a trade empire compared to what you get farming.

It's really quite simple:
If you have 5 trading guilds in 5 of your ports all trading with province X you are getting $100 or $180 or whatever it is per turn for each of the 5 trading ports you have usually.
So having province X as a neutral or ally trading partner earns you say $700-900 per turn. If you instead invade province X it would need to immediately yield you the same amount to just break even ....unlikely until you build it up....which also takes $$$ and time. Many provinces will NEVER yield direct income even close to what they sent you as trading partners.
Add to that all the other provinces owned by the former owner of province X now are at war with you so no trade with them either now. On top of all that you need garrisons for it now which cost build money and then maintainence costs.

You repeat the scenario above a few times all at once and if you were cutting it close on profit margins before your attack you will be quickly losing cash every year.

I keep all this in mind as I advance. Build those coffers up real nice to a point that a negative cashflow won;t kill you for a long while....then go dancing er....ahem...attacking