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...lets say with just the SB-700, if I had it buried in a softbox the flash itself may not see the preflash and actually not fire, am I correct in assuming this? Basically I want to be able to put these flashes anywhere and radio fire them and I think with that I most likely need poppers or something.
I used to use the Canon optical Master/Slave system, similar to Nikon's CLS, for all my multi-light setups. I found that in most home-sized rooms with light-colored walls to act as bounce surfaces my Speedlites would trigger even when inside my Westcott Apollo soft box, even with the diffuser down.
As rooms got larger I got more misfires, and outdoors it was virtually useless unless the Speedlite was in the clear with its slave sensor directly facing the Master.
Then Yongnuo released the YN-622C, an ETTL-compatible radio system, and all my problems went away. The YN-622C is transparent in use, in that all the "normal" ways of controlling the Speedlites via the camera's flash control menus work the same as if I were using the Canon system; ETTL autoflash, High Speed Sync, Rear-curtain Sync, Manual flash, etc. all work.
The YN-622C can also fire non-Canon flashes, even studio strobes via their PC sockets, either alone or mixed with Speedlites or inexpensive manual flashes like my Vivitar 285HVs.
Yongnuo has recently released a Nikon version, the YN-622N, that is similar, but because Nikon bodies don't have flash control menus (if I understand correctly) they operate a little differently and I don't know if they have as extensive a feature set as the Canon versions. It couldn't hurt to add them to your research list, though, and the price-point is considerably lower than that of Pocket Wizards or Radio Poppers.