For the vast majority 1 LLC and 1 checking (operating account for income and expenses) and 1 savings account (for security deposits and prepaid rent) and then as @Nathan G. says over here you might find a 3 account useful:  Do you have one bank account for all of your LLC?

In addition to closing costs, you'll also have 'pre-paids', which are the property taxes and insurance premiums you pay upfront at closing.

For example, If you're buying in August and the seller has paid their taxes for the full tax year (July 1-June 30) of the current year, your closing costs will include reimbursing the seller for 11 months of prepaid taxes.

Should I be crediting or debiting the accounts?

We have taken prepaid rent in the past but never at a discount. 

At closing we prorated the paid rents and taxes, but they were prepaid, not billed later.

total hard costs without points and tax or insurance should be $3056there are HUGE pricing adds for a cash out investor loan as Fannie and FReddie don't want to buy them right now.2.625 + .5 to points not rate right now 4.5 rate can get you to zero points or $4375 in points to get to "par"or 4375+3056= $7412FAR FAR cheaper in long term to get rate of 4.5 at no points and pay $3056 plus your taxes, insurance and prepaid interest which are not charges; just on-going costs.The difference in payment from 4.5 and 3.125 is pennies but $11000 is way too high. $3588 is not your property tax impound no way...You may find some lender won't want to do a cash out non owner as they can't sell them, then they price higher as there is a big risk to keep for long term.Go back to your lender and ask them about increasing the rate to 4.5 and give you better numbers. 

All of these will cover my closing cost and pre paid expenses.  

They do instant deposits to your bank account or free for 3 day wait as well as you can receive a Cash App debit card and just leave it on there and use as needed like a regular debt card.

There is another option from a mobile bill pay like Square, where you can manually type in a card number from any card that has a 'chip' or magnetic strip on it- like a prepaid Visa card.