I need to make 6 holes in floor joists for 3/4 pex pipe. 3 cold, 3 hot.
Can the hire and cold go together one above the other or am I only allowed one hole every few inches? I will be making 1" holes.

 

Short answer... holes must be a minimum 2" from joist edges, minimum 2" apart.

Of course this depends on your specific building code, (we aren't in Canada) but here is an example.

IRC R502.8.1 Sawn lumber.

Notches in solid lumber joists, rafters and beams shall not exceed one-sixth of the depth of the member, shall not be longer than one-third of the depth of the member and shall not be located in the middle one-third of the span. Notches at the ends of the member shall not exceed one-fourth the depth of the member. The tension side of members 4 inches (102 mm) or greater in nominal thickness shall not be notched except at the ends of the members. The diameter of holes bored or cut into members shall not exceed one-third the depth of the member. Holes shall not be closer than 2 inches (51 mm) to the top or bottom of the member, or to any other hole located in the member. Where the member is also notched, the hole shall not be closer than 2 inches (51 mm) to the notch.

 

Why run 3 separate lines? Why not just run one bigger line and tap off?

 

Can I make 2 holes directly above/below each other if they comply with the 2" rule? Joist would have to be 8" minimum to do this?
It's for 3 separate water heaters - 1 per floor.
Technically I could put all the cold from one pipe but the shut offs are per floor.

 

Yes you could do that if you have 2x10 joists. 2x8 joists are only 7 1/2. (2+1+2+1+2 =8"). An alternate code would have you separate adjacent holes by 3x the hole diameter.