There are two ways to record payment against Purchases:

Method 1:

Step 1: Go to Expenses > Make Payments, click on Add New Record.

Step 2: Select Against Purchases / Expenses.

Step 3: Fill in the required details:
Pay to – You need to select the vendor from the drop down.

 It will show the Purchase order with details such as Paid Amount, Outstanding Amount, Due date.
Enter TDS Amount, Payment Amount
Pay From account – Bank or Cash account information.
Payment Date – The date on which the payment is made.

TDS section – select if applicable.

Payment Mode- Cash, Cheque, credit / debit card, Internet Banking. 
You can select and fill in their respective payment instrument details.

Description – Users can add description at their convenience.

Step 4: Click Save.
If the user wants to edit/delete, they will get an option to Edit with delete option On the top right corner .

Method 2:

Step 1: Go to Expenses > Record purchases,

Step 2: Click on purchase number for which you wants to add the payment,

Step 3: Click on make payment and add the details of payment.

Step 4: Click Save.