Leveling your perks does not matter. Supposedly if you play long enough, you can get every perk.
As far as picking...out of what is available, what do you need or find most useful?
I started with extra loot/caps/ammo.
Did some damage on rifles, maxed out my carrying perk. Woot, now I can get fat and still fast travel to dump everything and go back and do it again.
Leveled pickpicking and hacking so I could get into more stuff faster.
Got lone wolf perk and dropped my buddy to carry more, take less damage, and do more...plus I have no more dumbass AI in my way.
Scattered a few about on levels I didnt really know what I wanted...point here in AGI, here in STR, int, etc...
Picked up the needed perks to set up supply lines and built all of the biggest shops/stores in my home base.
Think I am starting to look more into perks for modding armor and weapons, since some of those are needed for certain things you can build. Like you need gun nut perk for make level 2 machine gun turrets.