I generaly wait until the system is set up, all drivers updated and loaded, os, etc.. and running normal with no issues, all hardware everything showing up and working as it should, then I begin.
normally build, check bios flash if necessary, set basic bios functions and boot order, load os, update os, load all drivers necessary, add any programs for benchmarking, or testing, etc.. and start benchmarking for results and reference from stock normal running condition, temps are recorded, scores from various tests, etc..
then maybe a game or two loaded as well to use for real world tests.
After all that I begin pushing the clocks and watching the temps, I start with the cpu and fsb/memory, once I establish those parameters I then go to the gpu and push it a little too, depending on how the sytem overclock affected the bus speed to the card, but I am not familiar yet with pcie comapred to agp so that will be all knew for me.
Anyway I think doing it this way you can remove the guess work and have a reference for performance analysis and a good record of what your optimal settings were for the best overall system performance while remaining perfectly stable.
Good luck.
Lump