If your league penalizes teams for keeping a player, by requiring them to give up a draft pick, then you can fill out the "In Lieu of Pick" box that assigns the Rnd/Pk that is associated with that keeper player.
FanDraft will automatically populate that player into that selected location of the draft board.
In the example below, you will see Patrick Mahomes (QB) set with an "In Lieu of" pick for 5.2
On the draft board, "Patrick Mahomes" then appears in the 5.2 slot. The team will not have a pick there, as Mahomes has populated that pick.