To manually mark Purchase Invoices as Paid, please see the 2 options below:

1. Log in and from the Business page, click the required business.
2. On the Customer page, click on Purchases and Invoices and Credit Notes.
3. Find the Invoice you want to mark as Paid, click on the dropdown on the right side of the Invoice, select Pay, enter the payment amount, as appropriate, under the Paid heading.
4. To save the allocation, click Save. 

Please note, if you already have a Payment posted on the account to allocate to the Invoice, please follow the steps below, as completing the above will create a new Payment, which will cause a duplication.

     OR

1. Log in and from the Business page, click the required business.
2. Click on Banking on the left panel, select Payments.
3. Find the payment you want to allocate, and in the dropdown select allocation.
4. Tick the Invoice(s) you want to allocate to the Payment.
5. Click Save to save the allocation.