1) It seems that Vegas supports MPO format only from Sony cameras. In this case you can use “Pair with next stream” stereo 3D option. If your .mpo files are from Fuji then you can convert them to JPS format, which Vegas supports and use “Side by side (full)” option. For converting you can use MPO2JPS utility from MPO Toolbox (it’s free)
2) Afaik, there is no way to set media properties for multiple files in Vegas, except for the use of scripts (scripts can be used only in Pro version). For quickly changing stereoscopic 3D properties of multiple media files you can try Quick Properties extension from Vegasaur toolkit (it’s not free, but it has free 30 days trial period).