I think some of the scripts cause your money to be increased\decreased while the turn is ticking. therefore, you could be 10,000 positive when you click end turn but due to armies in the field, upkeep costs, character wages etc, you drop to a negative. then when your next turn arrives (5 min later:>) your profits (trade, merchant trade etc) are added to your 'negative' balance. So the answer to your question,, You must have too many units, or have a few in the field. Retire any units you dont need, or are outdated by other units. and only field an army when you need too. and build PORTS! and get those trade rights!Where did all my money go?
When i first played AD i had much the same problem, my economy was negative for too many consecutive turns. and had to restart the campaign. To keep your economy positive ONLY train units you need (don't train units merely because you have the money available), same for buildings. ONLY build in the settlements you need strategically. I also find building farms only when i want that settlement to increase a level helps.(from castle to fortress for example), that way your settlements wont populate too fast and you wont need to worry about 'squalor' too much. Which becomes a HUGE problem when you are negative for multiple turns!
My Current campaign i am playing as england and it is the year 1120 (81st turn) and i have not gone into the red yet. I have only taken 2 new regions, am currently planning a mass invasion of scotland while using diplomacy to keep the french on reasonable terms (i dont want to ally with them for the fact that i will eventually be invading them). Some of my regions have barely improved since the start of the campaign. i use 3 regions to produce my military and hire mercenaries to take care of rebellions. I focus on building up my economy by building those buildings first. Ive also found that rebellions seem to occur much more often in your outer regions, so my london region has never rebelled, but york has had a few. so if you expand your territory in a circle (so to speak) and move your capital to the centre of your empire that could help increase not only your economy but also decrease the rebellions.
Although the HRE i found is rather difficult to control due to its large size from turn 1!
Another solution if strategy isnt helping, cheat lol. go into the descr_sm_resources and increase the value of the trade items. which will bring in more merchant trade. or simply go into descr_strat and change the HRE's kings purse to a more favorable number Keep in mind that altering those numbers will effect the AI so they can benefit from the increased trade aswell!
Not sure if this post helped. i hope it did seeing as its so damn long haha...