Make it easy for you first, tenants maybe.I use deposit-only debit cards into my business checking.

Get them set up with a debiting service to collect the money from their account hopefully a day or so after they get paid.

If lots, then keep good records for contributions, draws and equity splits.Revenue:Rental IncomeOther IncomeExpenses:HOA FeesMortgage InterestProperty InsuranceProperty TaxesRepairs and MaintenanceProfessional Fees (such as accountants and lawyers)(Anything else on Schedule E that you doOther:Interest IncomeFlipping Business should include:Assets:Cash AccountsMortgage Escrow Account (if appropriate)Projects in Process (one for each project, ideally)Tools and EquipmentDeposits and Prepaid ExpensesLiabilities:Accounts PayableMortgage Payable (one for each property)Other Loans PayablePayroll Tax Liabilities (as applicable)EquitySame as aboveRevenue:Property Sales RevenueCommissions Revenue (if applicable)Cost of Goods SoldProject ExpensesExpenses:Most of your job expenses will be recorded in Projects In Process as an accumulated asset and then moved to Project Expenses when you sell the project, so there's no real need to separate out expenses such as Materials, Subcontractors, Holding Costs, Utilities, etc.  

Example (Dr = Debit, Cr = Credit):Purchase the property and rehab:Dr: Inventory - Acquisition Costs - $20,000Dr: Inventory - Rehab Costs - $80,000Cr: Cash (or loan) - $100,000Selling the property at a gain:Dr: Cash - $120,000Dr: Cost of Goods Sold - $100,000Cr: Inventory - $100,000Cr: Revenue (Sales) - $120,000Selling the property at a loss:Dr: Cash - $90,000Dr: Cost of Goods Sold - $100,000Cr: Inventory - $100,000Cr: Revenue (Sales) - $90,000In the third journal entry, your Cost of Goods Sold (an expense) exceeds your revenue which will translate to a net loss on your P&L.

You'll need to raise much more than that because you'll have to cover closing costs, syndication costs (remember the attorneys we talked about), any needed renovation or deferred maintenance that needs to be corrected, the first year's insurance will have to be pre-paid, utility companies will require a deposit (and for 100 units it's not a small deposit), the lender's tax and insurance escrow will have to be funded with a couple of months cushion, and you'll need capital reserves so cash flow isn't too tight. 

Prepaids and escrow account balances can skew this number. 

In addition, there are separate legal requirements for handling a security deposit, the failure to satisfy any one of which subjects the landlord to TRIPLE damages if it is raised in court.I just did a quick check for NY, and it appears there is no statute in regard to prepaid rent:NY Rental LawsBUT, when it comes to landlord-tenant law, it pays not to assume anything, so I'd strongly recommend contacting an attorney for a definitive answer.

My contract has pretty strict stipulations for reletting, and I think I will see the best 'value' overall by giving in and returning the prepaid rent once a new tenant is found.

We have a debit card on file for every tenant and we set up a recurring payment on the 1st Friday of every month.

2 months security, a co-signer, and have a debit card on file that you run the first Friday of every month for the rent.