Once you have drafted all six round in the minor league draft, you will have until a specified date to decide who you are going to sign to minor league contracts and who you are going to release (if any). If you do not complete these tasks by the specified date, the tasks will be completed for you automatically.
If you are under the 35 player limit and are under the league max, no changes will be made to your roster. If you do not have enough roster spots available, your coach will cut your worst players until you are down to the 35 player limit. If you are under the roster limit, but over the league unit max, your coach will cut the one player that will bring your payroll under the max. If cutting one player will not be enough to bring you under the max, he'll cut your most expensive player, then the additional one player that brings your payroll under the max.