Wow, this can be a very long discussion - but I'll resist.
There are 2 different ex system design theories: amplify the exhaust flow at a particular rpm point (usually peak power) through certain pipe lengths, diameters, collector design and collector dimentions. The second way (my favorite) is named 'anti-reversion' and has a design which tends to kill the exhaust pulse (which is amplified in the first design). Doing this dampening of the pulse tends to broaden the power over the rpm range. (I built anti-reversion headers for my sm blk Chevy dragster engine back in the early '80's.)
The most important dimension in header design is the diameter of the primary pipe, followed by the primary length and then the collector size and design.
Oh, the old separate pipe systems don't make the power of a collected system. (If it did, every drag car going down the track would have individual exhaust pipes - fuel cars excepted.) So, design a 2 into 1 collected system and put a Coanda cone on the end of it. Design programs should be able to be found on the net somewhere so one can set his pipe dimensions. By and large, longer pipes with not too large primary diameter are best, as they don't kill bottom end power and throttle response.
Stepped header design is an attempt to amplify the exhaust pulse over a broader rpm range, thus increasing overall power. It's tricky to design and build; they're best left to the pro header builders and, to me, are much too labor intensive to be worth it for a street engine.
By the way, putting a muffler on the end of an exhaust sytem, pretty much screws up the design, short of hanging on one of those specialty race mufflers, such as some drag cars use. (They're intended to kill noise, not ex flow.)
