Welcome to the site. A generic description on the e-mail draft will be below to help.
You can do what Dave says below (he is very helpful to dynasty league owners) To answer your question directly, though, go ahead and set your keeper amount and total rosters, go to
1. Commish Options>Edit Live Draft Options>Start e-mail draft>Draft your rookies... You will have players left over, just commish draft any players and then you'll remove them.
2. Commish Options>Edit Rosters>Select the team and remove the players where you want to stop the draft at.
3. Go to Commish Options>Edit Rosters>These are the keepers only (because you want to make sure they are kept for your next draft).
4. Then go to Commish Options>Edit Rosters>These are the complete rosters but still draft anyway
5. Then you can go ahead and schedule another e-mail draft