Assuming every team keeps the same number of players, just allow each team to keep the players and then use a set budget to fill the rest of the roster.
If you want to assign salaries to the keepers, you could either choose a service that assigns value (i.e. CBS or ESPN) or set a standard $ for each keeper (for example $10 in a $100 budget).
If you wanted to slowly convert from the 1st option (no salary assigned keepers) to assigning keepers salaries, slowly introduce the change.
For example, year 1 allow 3 keepers w/out salaries. Year two only allow 2 keepers w/out salaries, etc. After 2-3 years the transition would be complete.