New to accounting? See http://www.accountingcoach.com. You can learn virtually everything you need there. There are also some other good sites on the web. Before you can use Manager, you need to understand the basics of double-entry accounting. It's not just a bookkeeping program.
New to Manager? Read all the Guides. They are a work in progress, but getting better all the time. Before plunging in with your real business, I suggest creating a test business. (You can have as many as you want.) Experiment with a variety of entries and see what happens via frequent checks--as in after every single transaction--of the Summary, so you can see what happens. You can even follow through the accountingcoach.com examples by entering them into Manager.
As I said in my earlier reply, you have made some error in entering the payment received. Without seeing your books, I can't tell what it is, so you will have to track it down. As you do this, remember every blue number can be clicked to drill down and see what transactions contributed to it. I would start with your bank account(s) and find the transaction where you recorded payment. Look at what account you allocated the payment to. If it was anything except
Accounts receivable (and the subaccount for the actual invoice), you must correct that or it will always show as overdue.