I use Dia. I don’t entirely understand what you’re trying to diagram, so I’m not sure how well it would work for you. I’ve used it for data flow diagrams, state transition diagrams and flow charts, and occasionally for entity relationship diagrams and UML diagrams (though it’s not exactly good for those last two types). It’s easy enough to use that I prefer it over paper. I don’t think it has any way to automatically generate diagrams, though.
I use Dia. I don’t entirely understand what you’re trying to diagram, so I’m not sure how well it would work for you. I’ve used it for data flow diagrams, state transition diagrams and flow charts, and occasionally for entity relationship diagrams and UML diagrams (though it’s not exactly good for those last two types). It’s easy enough to use that I prefer it over paper. I don’t think it has any way to automatically generate diagrams, though.