The only way I know of marking without holding a marker in your hand, is with the ponce pad. This is a pad that you saturate with loose chalk, then gently go over a stencil with the pad, theoretically depositing the chalk in the design lines where it will stay until you remove it. I haven't used this myself yet, so I can't vouch for how well it works.
I haven't tried doing fmq with a marked pattern, as I think it would be difficult to stick to the lines. I'd be interested in hearing what others have to say.