Totally not silly. I use a drawing program (SketchBook), and very, very carefully draw what I want. Here's an example from my build thread (I think this took a good few hours to draw):
It's best that you figure out the pixel: inch/foot ratio that you want. that way you can draw things to scale. For example, each of the open spaces between the cinder blocks is 4' across, which lets me figure out that yes, I can have an inch of space between certain tanks, or no space at all.
I know other users have used Excel (still confused on that), Blend (the art program), and there are some really amazing ones where people have used Google SketchUp (I'm still wroking on my sketchup skills).
Did you ever end up making this set-up?