I don't think you're using your merchants to their max capacity. You will generate more $$ by acquiring other merchants than sitting on a resource, unless it's gold/amber. side query why is amber so expensive? you get more from amber that silver? go figure.

anyways, march your merchants along with a spy a few provinces away to skill up your agent to about 4 and then march into Milan area - it seems that merchants like to congregate there and acquire other merchants. depending on their level should generate anywhere from 500-2k.

as mentioned earlier the gold and amber are easy and rich resources, but if you are able, also target the spices and silk in Middle East - should generate 700-800.

Lastly, how do you get -80k at end of game? I normally play English and by the time I take out France, I'm pretty much rolling in $$.