RF diffusion _motif scaffolding with Target

[zarbuk]

Hi Everyone, I'm using RF diffusion motif scaffolding with Target and I had a couple of questions before I start my run. Can anyone please advise me on the following:
I have the structure of my enzyme with a single helix bound to the interface where I want to design my protein to bind. Using motif scaffolding with Target(which is the enzyme), I am trying to build the protein around that helix while keeping it intact and wanted to sue substrate as well as monomer ROG potentials.
I had teh following questions:
Are these potentials in conflict with the motif scaffolding with the target?
How do I define the relative position of C alpha carbons of the substrate with respect to the protein?

Is there a better way to approach this design strategy?
Please let me know if there are better suggestions and answers to my questions. I would really appreciate your help.