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PPD is points per day, the standard performance benchmark used for F@H. The benchmark machines complete CPU units at 110PPD and GPU units at 1500PPD.
It is OK to run two systray clients at the same time, so long as they have different Machine IDs. To find out (or change) the Machine ID right click the Folding@home icon in the system tray, click configure, and it's at the bottom of the advanced tab.
It depends on the unit, but I would guess that you would average about 250PPD on the C2D, and 2000PPD on the 4850, rising to over 1200PPD and 4000PPD respectively on the fastest units. The GPU figures will change as bigger units are released which utilise more of the GPU (see below for how that also helps to answer another of your questions). To calculate PPD the vast majority of us FahMon, which can be found
here.
To check that the GPU is actively working check the log file. (Right click folding@home icon | Status | Log file) If that is progressing then the logical explanation will be one commonly given at the moment: the current GPU units are too small to utilise the 800 SPs on your 4850, so it will not be being fully utilised, therefore reducing the temperature.
GPU usage at this point cannot be controlled, so yes, the only way to control that is to under or overclock. For the CPU go to the advanced configuration panel (Folding@home icon | Configure... | Advanced tab) and adjust the first slider. This can be done for the GPU but will massively slow it down as it does in fact limit the amount of
CPU the GPU uses to feed itself, and ideally it needs an entire core to keep going at a useful rate. This is however something of an anomaly as even slower CPU cores will keep the GPU fed at a sufficient rate.