So... my house (built in 1885) has gone through a few different types of heat before I bought it and so our ducts seem to have the same sort of spaghetti installation method.
What I plan on doing is to check out the ACCA manuals from the library, and make sure our system is correct from the start.
That said, there are some contractors out there who go by rules of thumb and the like, but in very old (or very new) houses, or houses where you've done some MMM style tinkering with insulation and the like, the rules of thumb are not likely to be accurate).
To start, you'd need Manual J (Residential Load Calculation) to figure out just how much energy your different rooms are taking in (and rejecting). Manual S (Residential Equipment Sizing) can help you figure out if your HVAC is actually the right size, based on the calculations from Manual J. Manual D (Residential Duct Systems) can help you get the ducting right.
As Heckler said, it'd be hard to calculate ducts you cannot see, but a few minutes with a flashlight can help you make some basic assumptions to get enough data for Manual D to be useful. That, and I think the manuals lay out the calculations in such a way that anyone with the ability to use a spreadsheet reasonably well should be able to do it.
In our house, the problem is mostly that two rooms (Master, my daughter's room) get a TON of sunlight, leaky windows, and have dormers where the insulation is still not the best. So, hot in the summer, cold in the winter. Balancing didn't work because the effective duct length was crazy after the 3 or 4 u-turns to get around existing gas / plumbing / electrical / giant steel beams that are in the basement. A little bit of science (and a lot of sitting and thinking about creative solutions) has helped me to figure out how to re-work the whole thing so that the upstairs bedrooms that need it most are pulling off the plenum where the pressure is the highest. (and also there are no more U-turns.)
(A mechanical engineer with an intense dislike of hack-job contractors and their "rules of thumb".)
One extra note... if you're going to go through the trouble of re-working all your ducts, make sure to seal them well. You may not be able to do anything about the bits in the walls already, but just making sure you aren't just pushing all your conditioned air into the basement will also help a fair amount.