To me the 500 skill point bonus is about the most worthless bonus offerred. Skill points don't really seem to impact the play that much, except when it comes to grades and ranks, and when you need 6400 to make LtCmdr 500 isn't really going to do much for you.
Now, to respond to your questions ... I would guess that they will be added to your existing character (much as you would add the Del Taco shuttle or TWOK uniform.
I highly doubt they have any impact on the skill point cap.