You can make a single payment in the Edit Registration page, and there a few ways to do this.
You have a guest that has registered for a Program that costs $1,690, and they have paid a $845 deposit. Their balance due is $845.
You can just click the Charge Balance Due button on the participants dashboard, and it will charge the rest of the balance owing.
You have a registration that you want to charge some specific amount.
You can create a new Payment by pressing Add Card Payment on the same participant's dashboard.
Then in the next page, add the amount you want to charge, and then save the Transaction, and it will charge the card the amount you specified.