Yes, right, your bank gets from Stripe only the net amount, as Stripe deducts fee before the payout. You can add an expense to your QuickBooks Online following these steps:
Go to theCreate button(Plus icon), and selectExpense.
Fill in the amount of a fee and all the other necessry fields.
In theAccountdrop-down, pick the appropriate one (most likely something like Bank Charges).
ClickSave and Close.
Another option I would personally prefer, is to use addon to sync your Stripe and QBO to automate all that and avoid manual work. Business Payments app for instance will create Sales Receipt (or Invoice accordingly) and the Expense which is a Stripe fee, so basically with that app all Stripe transactions should be accounted for properly and you are good to go for reconciliation.