When I apply my prepayment to my bill it create will create a Bill Payment Check. How Can I solve this?

Let's work on how we can apply the prepayments to the bill, sh2295.

When applying prepayments or credits, you just need to make sure that the AMOUNT PAID in the Bill Payment page is zero (0.00). This means that you are only applying the available credit or payments to the bill.

1. Open the affected bill.
2. Click Mark as paid in the Bill page and it will route you to the Bill Payment page.
3. In the Bill Payment page, you'll see the Outstanding Transactions and the Credits.
4. Mark the bill you want to pay partially and mark the credit that you want to apply.
5. Make sure the PAYMENT amount matches the credit that you want to apply.
6. Make sure the AMOUNT PAID in the upper-right corner is zero.
7. Click Save and close.

Now, let's correct the bills that are in question. We can delete the bill payment check that links the prepayment and the bill. Here's how:

1. Open the bill.
2. Click the 1 payment made (amount) hyperlink.
3. Click the date on the hyperlink and it will route you to the Bill Payment page.
4. Click More at the bottom and select Delete.
5. Select Yes to confirm the action.

From there, we can open the bill again and follow the Steps 1-7 that I've mentioned earlier. You can use this link for reference: Enter bills and record bill payments in QuickBooks Online.

Let us know how this goes so we can further assist you. Have a great day!

But my prepayment is 5000$ while my invoice is 10000$ so it create bill pavement check. And other 5000$ is still pending to send to vendors. So how can I solve this ?? 

What if bill amount and prepayments is different?