Are you using automated fills for the base pay? You will have to stop that and do manual fills on payday, or else edit the EOM fill after the fact to adjust the income amount to the actual pay deposited and allocate the additional income.
Or you could use a Projected Income account like I do. At the start of the month, do one Fill from New Income that puts your total base pay for the month into a “Projected Income” account and use that to fill all your regular envelopes for the month. On paydays, you simply record your paycheck as an Account Transfer from Projected to Checking. At the end of the month your Checking transactions will reconcile and your Projected Income account will be “negative” by the amount of your commissions and reimbursements. Simply enter an Income transaction named “Commissions and Reimbursements” that brings Projected back to zero. Now you’re at the start of the next month and you do the process over again.
You just need to be careful to check account balance before spending as the envelope balances will be based on income you haven’t received yet. It’s never been an issue for me, but it’s the thing that explodes heads when I suggest it 