How do you handle the party having a business?

Having to pay employees? Getting paid through the company?
If the business is illegal and has questionable sources, how do you represent the risk of those sources?
eg: Some sort of check to see if your spice dealers make you money

Are there any books you can point me towards?

Currently, how I plan to handle it is for each asset they will have an income, and a potential.

eg: Spice Dealer (200cr): Potential: 3

Investing in the asset, or insuring its safety, increases potential. Third parties messing with the asset lowers it. (eg: a rival gang could lower the potential of your spice dealers)

Potential would be rolled against an average check. Failure means no income, success means you get the income.

Check out the Far Horizons sourcebook, they have a whole chapter devoted towards setting up a business or homestead. Summary and review of contents:

Thank you!

I believe one of my players has Far Horizons (They played a Marshall in a previous game) so I'll have to steal that from them