If you need to pay back only a part of your debt, do the following.
1) Open up the debt account you want to pay off:
2) Swipe on the operation to the left, then you'll see two options: "Pay off" and "Delete".
3) Tap "Pay off". On the next screen with calculator choose a source where money comes from. Also you need to enter the pay off amount.
4) You'll see your pay off amount near the total debt.
Debts is an exclusive feature to CoinKeeper premium-users.
Now everything is done, you've returned a part of your debt!