Hey B1rdhous3!
Haha! It's a pitty, but not a problem, I just can deal with my raspberry at evening next day here 
I started hyperiond first from this folder but then I realised I could call it anywhere.
As I haven't uninstalled the classic Hyperion, I see that by default it boots the classical hyperion service (as you said). If I don't stop the classic and run the hyperiond, my LEDs get crazy.
So I believe I have to disable the classical hyperion service and enable the new hyperiond but I don't know how to do it (I am noob on Linux :oops:)
Thanks man!