I use gnucash for my self employment. I created a completely separate set of books from my personal accounting, which relies on having separate asset and liability bank accounts/credit cards. All business income goes into my business account, and from there I can make transfers to my personal. When I do this, I have to double-enter the transaction in each set of books, but it helps to keep business income and expenses totally separate.
The only business-specific functions I've used with gnucash is invoices (best doc I've seen is
http://linas.org/mirrors/www.aerospacesoftware.com/2003.06.21/GNU_Cash_for_Business_users_Howto_Guide.html), which won't apply to managing a rental.
The only other advice I have: come up with a logical way to organize your business expenses, but don't expect it to mirror your tax return exactly. For instance, if you have an expense that is not 100% business related, you can't model it perfectly. What I do is have all my expenses that I consider business-related done on the business side, then I can review them at the end of the year to figure out what qualifies for an IRS deduction, for how much, and make sure I have the required documentation.