The 5xxx seem to generate less heat than the 6xxx? [yes/no]?
Correct. Depending on which ones you have, the 6XXX series have multiple GPUs on them. I'd need specific models to actually assess the statement. As 5830s run cooler than 5850s, etc. It's all about the chips and how far you over clock them.
And there is heat pipes in the card, should i run water into them or something? lol
Um, no. The copper "pipes" conduct heat from the GPU up to the large heatsink fins. The fans blow over the fins and cool them. The only option you have for water cooling is if your GPU model has a water cooler built for it. Then you can remove the entire fan assembly from the card and replace it with a water block. However, not all GPUs have water blocks designed for them. Also water blocks add quite a bit of cost to the cards. It would probably be cheaper just to go with only 3 cards on the board, and get another board.