If there is enough air flow through your case then you may not have to watercool the motherboard components. Also depending on the setup, you may not need to watercool the motherboard. The key factor is
how hot does your motherboard get?
For Example: I have been using a Lian Li PC-V600 case (Very small for a "full ATX" Case) for my 939-pin AMD system (the motherboard is an Asus A8R32-MVP Deluxe). This combination didn't get that hot. However, I proceeded to "upgrade" the CPU, motherboard, and RAM. The second setup in the old case reported a motherboard temp of around 48°C! And that's not under a load, that's just idle temps.
The other factor involved is that each "bend" in a liquid cooling system slows down the "flow". So ideally speaking you don't really want allot of components on the same "line". What seems to work best is to start with a large (as in high capacity - or diameter) line, then have it branch into smaller lines for say CPU, Video Card, and Chipset. This keeps the flow through each line higher.