The only thing you can do for your pups at 2, 4 and 6 weeks is worm them.
I use Nemex2 (I get it from my vet). I am sure there are some people on here that give the puppy shots... (no earlier than 6 weeks, but it seems like most don't give the shots until 8 weeks). The only shot your vet is required to give your pups is the rabies shot.
Good luck.