When the payment comes into the bank (whether this is your current account or the virtual GoCardless account), you can click ‘Tag Me!’, select payment from client, and pay multiple invoices.
Follow the instructions, paying what’s left, and then simply select the option to leave the remaining balance on their account
Also have a look at a previous post by @Parker1090. This method also allows you to leave a remainder on the client account. The method works for sales and purchase invoices.