I have a business account that has checking, savings, and a money market account attached.
Checking account: Paying bills and cashing rent checks
Savings Account: Maintenance hold back, tax hold back
Money Market Account (higher interest rate than my savings): Deposits
I currently only have 1 rental, so my accounting is quite simple. At one time, I had 7 rentals, and I use the same system today as I did back then. Excel spreadsheet set up similar to a general ledger. Columns are labeled as
Date
Income/Expense (Drop down with both choices)
Type of Income (Drop down with: Rent, Fees, etc.)
Type of Expense (Drop down with: Maintenance, Improvements, tax, insurance, etc.)
Vendor Used
Amount of Income
Amount for Expense
Each tab was listed by the property name, and the last tab has totals
I built the formula for each tab so that it would calculate each column that needed to be calculated and provided me with a running total. The last tab calculated the running totals of the other tabs and it would let me see what my money was doing. I could show how much I spent on maintenance for the year, total tax payments, insurance payments, miles driven, etc. Doing it this way helped me when it came time to get with my accountant. She would go over everything to make sure we were deducting what we could, and then would handle the Texas Franchise Tax filing for me.
Good luck to you!