• Is there a rule of thumb out there that I can use to ensure that I have enough cooling capacity with my new Liquid Cooled PC?  For example, pump size and reservoir size vs what you are cooling.

 
I am building an LGA 1366 i7 - 980 with a GTX 580 3GB Hydro Copper 2.  The cooling system specs are as follows:
Thermaltake BigWater 850 GT (Came with Thermaltake Level 10 GT LCS Case)

• P500 Pump - 500 L/hr of flow
• Reservoir - 330 cc Capacity
• Radiator - 240 mm w/ (2) 120 mm Fans
• Hose - 3/8" ID

So how do I know when it is necessary to add another reservoir or pump or change hose size? Seems like there has to be a chart or an equation somewhere to help determine optimal system design.  Also, where should the coolant go first, GPU or CPU?

Well, I got a great deal on a brand new Thermaltake Level 10 GT LCS Case (Normally $369, got it for $150 brand new in the box), so I can always change out those components later, but out of date?  A pump is a pump is a pump.  I'm not using any Thermaltake cooling blocks.

ChallengerZZ
  A pump is a pump is a pump.  I'm not using any Thermaltake cooling blocks.

ok
the pump is known to go out after about 6 moths
so keep a watch on it, if your not cooling anything other then you cpu it will do fine as it is a low flow pump 
also do not use the TT rad, it is most likely made of aluminum and mixing metals is a big no no