Can you confirm you've exactly followed the steps described on the BodySlide mod page, under Troubleshooting -> #1 "How to use the program with Mod Organizer"?
I would add a point 8 to that list as well, which is pretty obvious but I'll mention just to be completely safe:
8. Whenever you want to run Bodyslide, do so through MO, by selecting Bodyslide from the executable dropdown (top right of the MO window) and clicking Run (same way you execute SKSE, Boss, etc.)
If you've followed their 7 steps, then when you run Bodyslide.exe through MO, it will have access to all mods installed through MO and therefore should see any custom armour mods you've installed in MO.
Note: I haven't used BodySlide or CBBE armours before, nor have I checked if the STEP guide provides its own instructions for CBBE/BodySlide. But I just checked the mod page, and the list of instructions it includes for MO sound exactly right to me, and the problem you describe sounds like it could well be caused by not running BodySlide in the correct way.
If you followed a different guide to using BodySlide in MO, could you a) link me to that guide b) cross-reference it against the instructions on the Bodyslide page, that I mention above, and see if there's any difference in what you did compared to what they suggest.
Edited by TheBloke, 12 June 2014 - 01:03 PM.