Shadow Bear's method is a good one though I'd add that the basic hull type (cylinder, wedge, etc) should determine the basic way that you lay out the interior floor plan.
I generally start with large blocks for engineering, the staterooms, cargo bay, etc and do the fuel last. Most decks are 3 m, but since the fuel tanks are more forgiving, they can be used on the edges to fill out the shape as you'd like it.
A method that is out of your price range by an order of magnitude is to use Canvas from Deneba Software (which is what I am using). I lay out the deckplans straight in Canvas (skipping the paper step from Shadow Bear's method). Two of the great things about Canvas is that I can set the grids to scale (so I'm working in meters with grid lines every 0.75 m) and Canvas will tell me the dimensions and area of any enclosed shape. Thus, when I draw out a block (or any other shape), I can immediately see its dimensions in meters and the area. My job would be very difficult without Canvas, but it's a bit much to own just for doing deckplans ($400 list). There is an intro version at $100 list, but I don't know what is missing from the intro version (probably nothing that is critical for deckplans).
Ron