You cannot apply the 90 boost to a level 90 (and presumably above) character. So don't worry about that happening.
You can apply the boost to an existing character on your account, or you can create a new level 1 character at the time you apply the boost.
If you boost an existing character who is at or above level 60, you get a Veteran's Bonus that boosts your professions to 600. You won't have to go back to level them, which is nice.
You pick a specialization during the process, which informs the starter gear you get."
