Was Troy in on the steroid deal? (Logan and other boy lying to Veronica for him) and did he just backstab his friend. Or did he "secretly" know about Other Boy's steroid deal and backstab them that way?

I think he "secretly" knew about Luke's steroid deal and backstabbed him that way. I don't think he was in on it directly. If Luke & Logan knew Troy was aware of it, I don't think they would've hesitated to tell V that Troy knew about it. I don't think they would've lied to cover for Troy, per se.