Allow me to jump right in and help with your question, mmp. 

Yes, it will affect your P&L. The best way of doing this is to use Undeposited Funds when receiving the payment. Then, add a line for the merchant fee when making a deposit to your bank. Make sure to add the merchant fee as a negative amount so it will deduct from the total amount that you received.

You can always reply to this thread if you have follow-up questions.