I received few cash payments from customers that I recorded, but never deposited into my bank. These funds stay in my "Undeposited Funds" register, how do I clear it up?

You can use the "Cash back goes to" at the bottom right-hand corner of the "Bank Deposit" screen where the "Undeposited Funds" (cash) is sitting. The cash back goes to your Owner Draw Equity account (Balance Sheet) because you did not deposit the cash into your bank account.

When you receive Cash payments you should have an option to have them go immediately into your Cash Account (may be called Cash on hand).  For your Cash deposits currently in Undeposited Funds, you simple need to make a "Deposit" into your Cash Account.

From your Banking menu select Make a Deposit.  Select your Cash Acct in the Drop Down Menu at the top (default is prob. your Checking Acct.) and then select the Cash items you want to move (if they don't automatically show up, try clicking Payments).  Then confirm the deposit down in the lower left. 

If at any time you have to much cash and want to make a deposit, from the Banking Menu pick Transfer.  Then fill in that the money is coming from Cash, how much and that it's going to your Bank Acct.