You won't see much of a difference either way, but having the coolant flow into the CPU block first will be slightly better. Once you have it on water, an extra degree or two on the NB doesn't really make much difference. Given the choice, I'd rather have the CPU a degree cooler.
As for the multiple loop question, if
THIS (or it's silver counterpart) is the system you're looking at, it's pump is going to be nowhere near as powerful as the MCP355. Or it's weaker brother, the MCP350. And with an aftermarket top, either one of those will almost certainly blow the P500 away. While the open-flow rate looks impressive, everything I've been able to gather about this particular pump suggests that it has poor head pressure, and TT seems to have gone out of their way to avoid posting it. And to be honest, if that pump was even on-par with the MCP355, yet drew only 7W like TT claims, watercoolers everywhere would be dry-humping the thing. A CPU and a chipset block, you'll be okay. Three GPU's as well? No. If you absolutely want a single loop, you'll definitely want a stronger pump (MCP355 or MCP655, for example), least the poor flow rates ruin your CPU cooling.