If You Use a Hoverboard on the Hoverboard Obby dose it count as you using the Hoverboard glitch

No, hoverboard obby you need a hoverboard. As long as your run is glitchless without you doing something to glitch a hoverboard ingame it is categorized as a glitch less. Of course this does not apply to other runs like Classic Obby than it will be a hoverboard.

I also think it might depend on the hoverboard used in the run. If it is the default hoverboard submit it as the glitchless and if it isn't or a shiny one do the hoverboard. Good luck on your run :D

Ty