I have a few carenado products including the Meridian, Phenom 100 all with the navigraph expansion. Is there anyway I can do a DCT to waypoint in my flightplan. If I do DCT it deletes all my waypoints in the flightplan.

Are you selecting the waypoint from the flightplan then pushing DCT or entering the waypoint after you push DCT? These are two different modes. The first will create a direct fix from your current location to the waypoint and keep the flightplan, the second assumes you're done with the flightplan and you want to fly to the new location.