When I filed my tax return in April I specified a direct debit date of April 14 and the debit was made on that date. If you file now with direct debit, you will be forced to specify the direct debit date as the date that you file, so you should be prepared for the debit to be made immediately.
If you pay online on the IRS web site (with Direct Pay) you specify the year that it's for. It does not depend on matching it up to your e-filed tax return.
