It took me a year to figure this out and about three painfully long drafts to finally perfect it. But it does work so here is how to go about doing it:
Under 'Setup' go to 'Draft and Rosters'
At this page you need to select 'Set Draft Order' in the Advanced Features
At the Draft Order page you need to Select 'Set Customized Draft Order' again in Advanced Features
Now you need to go through and set each round of the draft, entering keepers where appropriate. Once you do this, if I remember correctly, you can check out draft results and it will show the keepers. Good way to check and see if you entered all of them correctly.
During the draft those players will not be available to draft and will automatically be 'picked' in the round you set. It is rather time consuming especially if you have a large number of keepers but it does work.
Since I am actually contributing some helpful advice, I am going to throw out that if anyone is starting a new league on CBS you can get 1/2 off by using the promo code:http://cbssports.com/ref/38747310