We have a auction keeper league that uses a rookie draft, so no need to limit it to just dynasties.
We name our keepers (each team is allowed 3-5) one week before the auction.
We hold a 3 round rookie draft at the start of the auction, assigning players values based upon the round of the pick ($7,$5, $3). The draft order is reversed from the results of the regular season, with one twist: the winner of our Toilet Bowl (a play-off for teams that didn't make the $$ play-offs) gets the first pick overall, then goes back to his normal seed for rounds 2 & 3. This prevents teams from firesales via trades to playoff teams because all the non-playoff teams want a shot at ADP or CJ2.
We then hold our auction to fill the remaining roster spots.
If your keeper is a draft vs auction, then no need to worry about assigning salaries to the rookies.