Great question. There's a lot of ways I could answer this but I don't know enough about freeform these days to give tips tailored to that. I can try to make some statements about ttrpgs that might help though.
I've already answered a question on what to prep, or where to get started with making a dungeon. But for making sure the system gets integrated um, I think it helps to make a cheat sheet! It can be a bit of work but I have a cheat sheet for Robins where I copy and pasted the rules I needed on short notice from Songbirds and Robins because I didn't want to remember page numbers. If you are using a vtt like roll20 then you can just upload screenshots of the rules and just put them on the board. That way everyone has eyes on the rules at any time and can pick up when they should be included in play.
