A bookkeeper might get $15.00 an hour on a salary, you need to profit after taxes over that including employee expenses to be profitable.Most in RE are usually buying a job, see if your "earnings" are on par with similar job functions, you may be under paid!

I am not very experienced with book keeping or accounting but it seems to me that security deposits and refunds are liabilities for the balance sheet but not income and expenses.

Enlist the help of an experienced bookkeeper or accountant.  

I have all of the necessary connections in to put into place (online and drop off payment options, maintenance company, yard care company, attorney and book keeper) to piece this together.

Even my bookkeeping business is done mostly from here.

Xero, a Quickbooks competitor, has a less expensive "GL Only" version, but it's only for accountants.Zoho Books is cheaper than Quickbooks and probably can do packages (I've used it as part of Zoho One, NOT on its own).AccountingSeed, a Salesforce native accounting package (but can be bought without Salesforce) can do multi-business roll-ups and track multiple journals, but it's dramatically more expensive than QBO.I think Netsuite would suit your needs, but also more expensive.I will say that "Many LLC Books" problem has been an issue with EVERYONE with the move to Cloud.

and bookkeeping (tool for this?) 

@Michael LeeI use cozy for rent payment and beaver for bookkeeping and preparation of Schedule E. 

  #3, My RE business in its current state (9 units) urgently needs an CPA/bookkeeper, so fund management experience should be a criteria in our search. 

Who is handling the financials/bookkeeping?