I have an account that requires me to pay it bi-weekly instead of monthly.
This site is based on accounts with monthly payments, but there is a way to workaround the problem. First, change the due date of the account to the end of the month. Record your payments as you normally would, but you'll have to override the payment amount. When you make payments, keep an eye on the due date. If your payments are over the minimum payment due amount, the due date will get bumped up to the next month; just go into the debt details page and change it back to the end of the current month.
Here's a blog post that goes into more detail.