The notice you referenced allows the 401K to split the distribution/rollover into separate accounts so the after tax amount can go directly to the ROTH and the pre tax to the Trad IRA ... however if you did not take advantage of that option when you converted the 401K to the IRA then a form 8606 should have been completed at that time and any future distributions must be taken out as a ratio of taxable/non taxable using the 8606 form to compute those parts ... you cannot just take out the after tax contributions by themselves.
