Some customers pay into our suppliers account instantly gets a 6% rebate, my company gets 2% commission at end of month. What's the best way to record such transactions?

A pleasant day to you, ahmedel_rahi.

You can create two different service item for the rebate and commission. Then, add them as line item on your invoice. Let me show you how to perform this by following the steps below:

1. On your invoice, enter the items.
2. Under items, click the drop-down arrow to Add new line.
3. Choose Service.
   
4. Fill in the necessary information and click Save and close. Do the same for the other item (Commission and Rebate).
5. Add them below your items and make sure to enter the amounts as negatives. This is to deduct the percentage to the invoice amount.
6. Review the information. Then, click Save and close.
   

You can also visit our guide about managing items in QuickBooks Online: Add, edit, and delete items.

Get back to me if you have any other questions. I'm a post away to help. Have a great day!