How do I set the round cost for keepers?

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 the player was set with an "In Lieu of" pick for 2.2

On the draft board, the player then appears in the 2.02 slot. The team will not have a pick there, as that player has populated that pick.