You can subsidize shipping lines, which gives them some cash to get on their feet. AFAIK, they only use the cash to build ships. I usually give each line ~10k and they handle the rest.
Also, when your wealth is above zero, everything operates normally. When your wealth turns negative, EVERYTHING slows down based on the Economic Production Modifier, which drops slowly from 100% to 0 based on how deep in the hole you are.
Anything you do costs, usualy on a one to one basis
A factory, that costs 120 minerals to build, also costs 120 wealth A research lab, that provides 300 research points per year, also costs you 300 wealth per year to operate A ship that costs you 800 build points, it will cost you 800 wealth to build