Just to be sure, can I submit flash games I made in Stencyl? Thanks. 

Yup, any game works as long as all of the assets are original. You could even make a game in an engine that doesn't use code, like Click Team Fusion.

Thanks for letting me know! 

Yep! Just make sure it can run easily without having to install extra components. So an executable file or hosting it on the web etc..