Ok so the SPECIAL and Perks system works like this-
You start the game with 21pts to add to any SPECIAL category, and each category starts at 1, so 28 total.
Once all are applied you can do things in the game (kill, craft, etc) to earn exp towards getting a new perk. You also earn exp towards leveling up and getting a SPECIAL point. These two things are not related to each other. I've gotten multiple extra perks but only one SPECIAL point so far.
You can select any perk available, regardless of level. For example, the first time you level up to a new perk, it'll ask what you want. If you have say a 5 in Endurance and a 2 in Strength, you are allowed to select any perk up to Endurance's 5th perk. The 1st available, the 4th, doesn't matter. But you cannot select the 7th or 8th because your Endurance is a 5. Where as if the Strength is a 2 you can only select one of the first two options and only those. So it's cool that you don't have to go in order, you can pick any one you like within the range of your SPECIAL.
The perks themselves level up to stronger versions. So say you have the perk where sneak attacks to 25% more damage. That perk can level up independently to have 50% more damage. Then 75%. Then double damage in its final form.
You'll have the option of changing your SPECIAL arrangement before you leave the vault at the exit door, but after that it's set for the game.
