The bulk of your time during the draft will be spent in the Draft Pool. This is where you have access to every player in the draft. You can sort/filter them in virtually any way you like, you can target players, and you can bring up their player cards to store notes on players.
The main view looks like this:
The list is sorted by position when you open the pool because OVR is defined by you and may not be present.
Filter By Position is fairly self explanatory. Choose a position (or position group such as DL, OLB, etc.) and click Go and the pool will display only the players that play that position.
Filter By Ratings allows you to view only players that meet the criteria you choose. Pick a rating, an operatory to apply (less than, equal to, etc.) and a value and click Go to filter the draft pool.
Targeted allows you to filter the draft pool based on the targeted status of a player. Yes shows only players you've targeted. No shows only players you haven't targeted. Meh shows both.
Status allows you to filter the draft pool based on whether a player has been drafted yet. Available shows only players that are still available to be draft. Drafted shows only players that have already been drafted. Meh shows both.
Target A Position allows you to target every player at a given position.
Delete All Targets does exactly what it says.
The player table itself allows you to sort by any of the columns. You can sort in either direction by click the column more than once. The green + and thered X are for quick targetting players. The + is to quick target. It opens up a new window which you can immediately close. In FireFox I can hold down Ctrl (to force the link into a new tab) and click a whole wack of players all at once to quickly target the players at a position that I like. Shift in IE does the more or less the same thing. Clicking the X un-targets a player in the same fashion (new window that you can close).
Clicking on a player name brings up his player card. It doesn't really give you new information, but it allows you to store notes about the player and save them. This targets them and stores the text you typed in. Quick targeted players get "Quick Targeted" in their notes section. At the bottom of the card you can also see the Unique ID of the player which is needed for the Head to Head comparison page.