I have tried that and wonder about the same thing - but apparently it is a NO-CAN-DO !
The system was supposed to work with the lowest published fare - but butting heads with the system it only shows one fare !

Suggest scrap the employee discount and go directly to Delta.com and book the lowest fare possible and with the cavet of having
to pay the check baggage fees you will with a greater percentage of the time come out way ahead of the game. Have the America Express
Card tied in with Delta use it and the bag fees should be waived on at least the first bag and the miles that go with the deal.
The Fly Confirmed for Less ticket does not award miles which the other discount program does.
The Fly Confirmed for Less program does give a slightly better discount but when compared to the Delta.com site fares WHY BOTHER !
The ONLY way I would consider using the employee discounted fares would be IF there was a menu of the published fares to be selected
and it has to be a significant savings fare reduction which it is not at the present !

Another undesirable feature about the Fly for Less Programs is you buy a coach ticket and can not use any of your employee benefits to
UPGRADE to the front cabin if seats are available ! A very personal sour note !