When someone pays you via stripe you record this payment (whole sum) as money in in your stripe merchant account. After that you have to record a second line but this time money out, and that is the fee stripe charge you. For example you get £35, than is stripes fee £0.69. So, from the original £35 you get £34.31. Seven days later you get a payout from stripe which will show (if you use auto-bank-feed) in your current account, if not you write manually a money in line over £34.31. Then you tag this line as a transfer between accounts (choose your stripe account) and you are sorted. To make things easier you can apply a rule to auto tag these transaction
I think you’ve got your ins and outs reversed here - invoice is paid in full into the Stripe holding account, net settlement is a transfer from holding account to current account, and the monthly fee invoice from Stripe is then paid out of the residual balance on the holding account.