http://fantasygames.sportingnews.com/stratomatic/about/popup_faq.html#autodraftworks
Basically, you will put a draft list together on the TSN/SOM site as if we were doing the Salary Cap Auto Draft.
You will list your final 10 player choices (which must be players not already claimed in the draft) in order of preference in the first 10 positions on your draft card. The remaining 15 spots you will fill with the players you drafted on Diamond Dope. You must have 11 pitchers and 14 hitters on your draft card. See the link above for how the draft will run.
After the Autodraft, there will be a period of a couple days for you to see which of your 10 player choices you actually got and which you didn't and to plan roster moves accordingly. You will set up waiver claims during this time. After the waiting period, waiver claims will be awarded and from that point until the season starts, you will be able to add and drop players (within salary cap constraints) as much as you want.
The link should help you find other answers you may be looking for.