Payment and Settlement in Rebate

Dear Gurus,

Can any one explain the difference in b/w rebate payment and the settlement.

at the time of invoice rebate created with rebate expense debit and rebate payable credit lets say by $50.

when i did manually payment system create a credit memo request of lets say $50 and post a credit note, only one line of condition type appear in the credit note, and entry made of rebate payable debit $ 50 and customer credit of $50.

if i made the final settlement system again take into account the above figure which i assume is not correct.

Looking for the advise, so that problem can be resolved.

Hope gurus will see this.