Assume advance is $10,000
1) Create a New Expense
2) Select Supplier
3) Select any payment account (it doesn't matter because expense will net out to zero)
3) Line 1: Category Accounts Payable / Amount = 10000 / Sales tax - Out of Scope
4) Line 2: Category Shareholder Loan / Amount = -10000 / Sales tax - Out of Scope
5) Make sure total expense is zero
6) Save and Close
Subsequently you get bill for 25000
1) Create Expense for 25000
2) Assign expense category
3) Enter Amount
4) Save and close
Subsequently you pay the net amount which is 15000
1) Go to Expense > Supplier > Click Supplier
2) Find open Bill of 20000
3) Click Mark as Paid on the right side
4) Select Bill and Credit
5) Payment amount should be 15,000
6) Save and Close