The key distinction is that the Draft Assistant w/Sync connects directly with your drafts on Yahoo, ESPN, CBS Sports, NFL.com, MyFantasyLeague, Fantrax, RTSports, and FFPC to automatically cross off taken players.
Our Draft Assistant w/ Sync tracks taken players for you, so there's nothing for you to do except connect to your draft and click the Refresh button when you want to force an update (recommended approach) or select "Auto-Sync every 30 seconds".
For the Manual Draft Assistant (which can be used with any site), we offer a dead simple way to manually track your draft. Just start typing the drafted player's name and he'll come up through our fast player search. Or, you can simply note that the player has been drafted through the drop down link next to each player's name in your cheat sheet and player queue.