If you have payments sitting in undeposited funds that you deposited manually, you need to clear them out.  You can delete the deposits you made without using undeposited funds and then deposit them correctly, but this will affect your previous reconciliations.  The beginning balance of your current reconciliation will change and the newly entered deposits will show up.  They offset each other, so all you have to do is check them off to finish your reconciliation.  However, this means you'll have a reconciliation report that doesn't match your bank statement.

So you might want to do the $0 deposit trick instead.  Go to Banking > Make Deposits, select all the undeposited funds that have already been deposited, then add an additional line on the deposit with a negative amount (bringing the deposit total down to $0) using whatever account that was used on the manual deposits (most likely a revenue account).  No effect on your checking account, but it’ll not only clear up undeposited funds but also the duplicate revenue you most likely created when you entered your deposits manually.

If you use deposit the $0 check to your regular checking account, you will see a $0 deposit that you should clear on the next reconcile.  For this reason, I prefer creating a "clearing" bank account that I used for all my $0 transaction tricks.