Each skill has 5 skilllevels, some skills you can learn from the start and to get the skill to level 2 you have to meet a level requirement. I.E.:You can learn Sword Expertise from the start of the game, but to increase it to level 2 you have to be level 7.
Other skills only become avaible at a certain level i.e. Deadly Gift level 1 can only be learned once you reach level 6. for level 2 of Deadly Gift you need to be level 12 IIRC.

Identify is indeed passive: when you hover over an item or press the alt-key the item will be identified if your Identify skill is high enough. So at the start of the game, you're not able to identify any unidentified items. When you get the first level of the Identify skill, you automaticly identify items with Identify level 1 when you hover over them. A text should appear: Item identified.
If you have only level 1 of the Identify skill, items which need level 2 and upwards to be identified will still be marked as unidentified, so you have to either raise your Identify skill, or let a merchant identify the item.

[Linked Image from miniprofile.xfire.com]