The first thing you should do is a web search using: video card water cooling guide.
The stock video card air cooling setup also cools the video card's memory and VRMs.
A video water cooling setup will need to cool these components too.
You need to consider how many motherboard slots will not be accessible with either cooling option.
An air cooled dual card setup presents additional cooling challenges especially when you have additional plug in cards installed next to the video cards. I have a sound card installed below the lower video card in my SLI setup and the lower card's gpu temperatures are ~ 5o (C) higher than the upper video card. I have an additional 92mm cooling fan that draws outside air from unused drive bays and directs the airflow to the top and bottom of both video cards.
For simplicity, lower cost, and a cleaner looking setup I think that using a higher end single card setup will be best.
my 1+1 cents advice.