For a start, SkyBox haven't implemented MVC support yet, so this would at least need to be in place first.
Currently, to watch 3D Blu-ray (or any Blu-ray) in SkyBox, you first need to rip your Blu-ray to your hard drive or NAS (media server).
I use MakeMKV to rip my Blu-ray discs to a single .MKV file for media player playback (I then catalog / browse them using Plex).
However, due to lack of MVC support, SkyBox still cannot play the 3D Blu-ray .MKV rips.
For SkyBox to be able to play your ripped 3D Blu-ray, you currently need to convert the 3D rip .MKV file into a Side-By-Side .MKV file. Unfortunately this is a lossy / image degrading process, in addition, it adds to your storage space requirements by needing you to create this lesser quality duplicate copy of your 3D Movie (you don't want to delete the direct Blu-ray .MKV rip file, as this is the original quality MVC encoded 3D movie file).
So, for this step I use BD3D2MK3D. I de-select the "Half" checkbox, which otherwise immediataly halves the horizontal image resolution. I also select "slower" and "18" in the settings, to provide an acceptable? outcome from this lossy re-encoding process.
After conversion you have another .MKV file which is 3840x1080p (twice width for left + right images side-by-side).
nb. Make a note of the forum topic on file naming conventions.
This SBS file will now play as 3D in SkyBoxVR! However, there are still a couple more SkyBox issues to deal with. When you initially select the 3D mode for 3D playback you end up with a squashed 32:9 aspect image, so you then need to go into the advanced settings and select 16:9 Aspect Override. Then you are all good for watching in glorious 3D! :-)
However, there is still one other issue in that SkyBox doesn't currently retain this setting, so everytime you view the 3D movie you need to again go into the advanced settings and select 16:9 Aspect Override!
Finally, I do recommend using Plex server to catalogue / serve-up your files to your media player(s). By enabling the DLNA server functionality in Plex, your Plex server will then appear in the Network menu in SkyBox, and you will be able to nicely browse your Plex catalogued movies via organised folders.
Hope all this helps. You might also want to add your vote for MVC support to the "Support for MVC 3D file format" topic.