There are so many variations that you really need to figure out what type of keeper league it is that you and your owners want, each having pros and cons:
Is it a dynasty (keep all players), a fixed number (everyone must keep the same number of players), a max number (everyone can keep up to x number of players)?
Is there a "cost" involved, such as draft pick forfeiture? If so, what is that cost based on, is if Player 1 is your 1st round pick, player 2 is your 2nd round pick, or do you forfeit the pick they were drafted in (and then what is cost for FA pickups)? Do you charge the round plus X , so for example if x is 2, then a player drafted in the 4th round could be kept for a 2nd round pick the following year, etc.
Do you want to cap how many years in a row a player can be kept?
That was just a couple of the things off the top of my head that need to be addressed (I'm sure there are a lot more regarding just the keeper aspect that will come up as you work through those), but those lead to additional rules questions, such as the trading of draft picks (allowed or not, and if so how many seasons into the future), when are keepers declared, can you do trades between season end and keeper declaration, etc.
Also, need to decide if draft order is based on previous seasons finish or not (in general, the more keepers there are, the stronger the case to have previous seasons finish determine draft order, the less keepers, the more it can be argued that a more random order is fairer).
You know your league best and what they are looking to do, so as you come up with some of those answers can help you figure out what other things you need to think about based on those decisions.
