To bypass - when it gives you a choice of payment options for your Federal tax due, select "pay by check" and then you can just ignore the voucher that prints up for you to pay because you have made other payment arrangements already with the IRS.  The IRS won't be expecting you to pay in full just because you select that option - that information isn't sent to them, its just a trigger to print up a voucher form for you to use to send with a check.