The taxes you owe on your income for the year are not actually computed and paid until you complete your Tax Return, so you are not being taxed twice on your commissions.

All of the tax withholding from your paychecks and commission checks are totalled together and reported on your Form W2.  Think of the withholding as paying towards the "tax liability" that is calculated on your Tax Return.

All of your federal tax withholding will be reported in the "payments' section of your Tax Return and be netted against your tax "liability".