For the mark VI boots, should i get the 3 piece one so i can fit my shoes in there or the 2 piece boot?
Go with the 2 piece boot. If necessary, you can cut it into a 3 piece boot. The two piece boot fits together a little better than the 3 piece boot.
This questions kinda random, and I didnt exactly know were to put it. but can you hear anything inside the helmet with the padding and stuff.
Yup.
what did you guys use for the weird side vent "tubes" hes got near his chin on the MK VI helmet. Oh and also, how do you put lights in the helmet ( I do know how to solder and all the ). Do you put them in during the pepakura stage?
You can get some flexible conduit from any home improvement store, and then fit it in.
Lights go in after the helmet is hardened and shaped. Solding isn't too hard, but it does take practice.