It seems like the dual/triple boot option using noobs isn't working properly for me (SD-Card issue???)
I wiped my OSMC kodi install from my SD card and installed Retropie 3.3. From there I use the kodi "app" to get to Kodi. Once there, the wifi android remotes work as they did before.
I have managed to set up the ps3 controller(s) to pair over blue-tooth successfully. This process is actually pretty straight-forward in RetroPie.
This saves me the hassle of switching OS's every time.
Now all I need to do is check is if my ps3 controllers can be configured to control Kodi.
UPDATE In the meantime I do it the other way around. I install OSMC and on top of that I have installed the retrosmc project. This starts emulationstation from Kodi. Works well for me so far, if not a bit more stable.