Lycanthropes as Characters states:
Racial Hit Dice: A lycanthrope adds the Hit Dice of its animal form to its base Hit Dice for race, level, and class. These additional Hit Dice modify the lycanthrope’s base attack bonus and base saving throw bonuses accordingly.
Level adjustment: Same as the base creature +2 (afflicted) or +3 (natural).
The rules for Monsters as Races, along with the rules for Increasing Hit Dice tell you how to do this.
Essentially, the extra hit dice are treated like levels in terms of acquiring feats, skills, and attribute bonuses, as well as being used in calculating Base Attack Bonus, level adjustment, and saves.
For example, suppose you had a level 2 paladin:
Hit Dice: 2d10 + 2 * con
Skill points: 10 + 5 * int
Attribute Bonuses: 0
Level Adjustment: +0
Applying the afflicted Werewolf template gives you:
Hit Dice: 2d10 + 2d8 + 4 * con (As adding two levels of cleric)
BAB: +3 (As adding two levels of cleric)
Fort/Ref/Will: +6/+3/+0 (As adding a class with good Fort/Ref saves)
Feats: 2 (as a fourth level character)
Skill points: 14 + 7 * int (as adding two levels of cleric)
Attribute Bonuses: 1 (as a fourth level character)
Level Adjustment: +2
ECL: 6 (two levels paladin, two wolf hit dice, level adjustment of +2)