I prefer to use the estimated wing loading as my guidline when building. I like this little calculator here:
http://www.flyrc.com/wing-load-calculator/
The "wing cube loading" factor gives a very good idea of the flight experience you will have. I also use the WCL to estimate the minimum power required. Higher the factor, the more power required to make it enjoyable to fly.
For example, the little scratch built DH.88 I made for the "buildruray" has about 80sq" of wing and weighs 3.5 oz. That means that its WCL is about 8.5 which is about right since it isnt overpowered by any means.
The rest of the proportions are generalizations to use when trying to go for certain flight characteristics. For the same WCL, more chord vs span will give a more sporty feel. You'll have better roll but a less efficient wing. A longer wing will be more efficient (like a slope soaring glider) A shorter coupled plane will be more pitchy and, because of the leverage, often requires larger tail feathers to maintain good stability. A longer fuselage will be much more docile and will be more forgiving about the CG... From there you can start getting into different types of air foils, leading edge flaps, and on and on, but then we are entering a new bottomless rabbit hole...