@Kimberly74 

Stripe fees are an expense (Merchant Fees), not COGS. 

This really depends on how many invoices you're processing and whether you use bank feeds to match the deposits to the invoices/payments.

If Stripe deposits each customer's invoice payment separately (or you don't have enough transactions where the deposit is a combination of multiple invoice payments), and you use bank feeds to match the deposits to the invoices/payments, then create a Service or Other Charge item called "CC Processing Fees" (or something similar) and select the Merchant Fees expense account (set one up if you don't have one) as the income account on the item.  Add that to the invoice as a negative amount so the invoice balance matches the payment/deposit.

If Stripe combines customer's payments in a batch or you don't use bank feeds to match the deposits to the invoices/payments, you can create a separate expense transaction (New > Expense) for each week or month to record the total cc fees for that period.  This makes it easy if you process a lot of transactions because you only need to make one expense entry for all payment fees for a given time period.  It does make your bank reconciliation slightly more tedious but IMO it's easier than adding the cc fees to every single invoice.