Camera Labs

I currently have 2 SB-600's, and I'm thinking of getting an SB-700 as well. I am however, having some problems triggering my flashes, since I tend to position them in positions that are "inconvenient" to the CLS system.

Therefore, I'm looking into radio controllers, namely Pocketwizard's, but I'm not entirely sure of how they work. Currently, I can control the strength of the flash output by using my D90's built in commander function. If I get a PW, can I still use the same menu to control the flash output? Or will I be forced to actually go to the SB-600, and physically change the power setting on the flash? Or can I change the power setting on the transciever? (I'm used to shooting on manual power, so the TTL-function isn't something I'm going to miss)

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Nikon D90 (Primary), Nikon D40 (Backup)
AF-S DX 35mm f/1,8
AF-S 60mm f/2,8 micro
AF-S DX 55-200mm f/4-5.6 VR
2 x Speedlight SB-600

To use the TTL Metering system, you will need a compatible trigger set like the Pocketwizard mini/flex. I am not sure though whether the camera's menus will work or not to control it. I know they have a 'zone controller' to set ratios.

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Canon EOS 500D
Lenses: EFS 18-55mm IS, EF 50mm F/1.8 II