I am not answering as a church bookkeeper, but with my job, we utilize Venmo, Stripe, etc.  I post a sales receipt (credit the "Sale" and debit "Undeposited Funds" for the amount).  Then when Venmo, Stripe, etc "settles" (deposits into bank), I will record deposit amount which debits the bank account and credits Undeposited Funds for the sale and the fee is a credit (enter as a negative number)  to an expense account (merchant fees or whatever you choose to call it). The amount should agree with the amount that went into the bank account.