Sometimes your customers owe you money, but they just don't have all of it, so you'll take a partial payment for now. For those cases, we've implemented the new "Manual Collect" feature, which lets you collect their payment method on file for the amount you choose.
One word of caution, though: With great power comes great responsibility. Collecting this way won't automatically keep your invoices in sync, so you will probably end up in a situation where you haven't issued the invoices for the payments you've received. Just something to watch out for when you do your accounting.
That said, this can be a useful tool to get at least some payment when your client isn't able to pay the full amount.