So I've really been researching all the skills and working on builds but one part is confusing. You automatically start with one point into each skill tree then add your 21 however you see fit. My question is if you don't put any points into agility for instance...you still have 1 point in it automatically. Do you get the first perk for the agility tree even if you don't bring it to rank 2?

Yes. How is that confusing? There are ten perk options for each SPECIAL stat, one for each point. If you start with 1 AGI, you have access to the tier 1 perk. If you start with 2 AGI, you have access to tiers 1 and 2.

You don't get any perks automatically by fulfilling their S.P.E.C.I.A.L. requirements, you merely get access to them. You need to spend a point when leveling up you character to actually activate or level-up a perk.

So you do need to be agility 2 to unlock the perks. You have to add a point

With agility 1 you have the possibility to unlock the first level perk for agility by spending one point. You cannot unlock higher level perks, unless you increase agility first.

Are you asking if you get the perk or have access to it? SPECIAL points only give you the option to spend a perk point on a certain tier of perks. If you have 7 AGI, you have access to the tier 7 perk in the AGI tree, but you still need to spend a perk point to actually obtain the perk. You don't need 2 AGI to obtain the tier 1 perk.

The Fallout wiki is a great source to check out what kind of character you want to build. http://fallout.wikia.com/wiki/Fallout_4_perks

I already know that I want to build an Intelligent and Charismatic character

Also, you don't need to take tier 1-5, in order to take the tier 6 perk for instance. You can go straight for Tier 6 if your SPECIAL stat is high enough and you have a perk point to spend.

Each perk also has multiple levels, just like in the old games.

I think the OP has he system a bit confused. First off, it's not a skill tree but a perk matrix (SPECIAL attributes at the top and Stat values down the rows). You do NOT have to learn the perks in any order. You just have to meet the requirements and have a perk point to spend.

• You get perk points by leveling up (1 per level). There may be other methods to gain points (like reading books / magazines, etc.)
• You can either spend a level up point on either a new perk or rank (you meet the requirements for) OR increasing any SPECIAL stat by one.
• Most perks have multiple levels or ranks (you can learn the perk multiple times to improve the perk).
• You must meet the requirements of the perk in order to learn it. The base requirement is that you have a certain SPECIAL (column) value for that perk and then most higher ranks have additional requirements (like character level requirements).