For a SINGLE payment like this:

And a Bank Statement with TWO lines for that payment like this:

You would reconcile like this:

In this case, I am reconciling the $105 payment (in blue) with the $5 line (the first of the two lines)

Then, I reconcile the “RECYCLE THE $100 TO REUSE IT” that was put back in the Account Receivable account with the $100 line (the second of the two lines):