Average flow is what matters for the most part. But a flow bench cant really give you an idea what the velocity is. You can grab a weld stick, energize a welder and touch it to a ball bearing. The ball bearing welds itself to the stick and now you can use this as a tool for finding dead or slow areas in the runner. You move the ball around in different areas of the runner and see if the flow goes up or down. If flow goes up when you block a given area, then that area is dead and not contributing to flow very well, and it can give you an idea of what to do, where, and why. Reher Morrison builds pro-stock engines and has for many years. I was reading an article from them, and he was talking about 2 different sets of pro stock heads that flowed the same numbers, end to end...get it? from .100 all the way up to an inch of lift, they flowed basically the same. But one set made 150hp more than the other set.
What matters the most when porting heads, is to match peak port velocity with peak torque rpm. If a port is really big, then when the intake valve cracks open and the piston starts to draw down, the column of air will be really slow to accelerate. Even when the piston is halfway down and at its highest speed, it still cant accelerate that air column very fast. Then after bottom dead center when the piston starts heading back up, the charge has so little inertia that it stops flat and stops filling the cylinder. With a smaller runner, the intake valve cracks open, the piston starts drawing down, and the air column accelerates very quickly. The speed of the column matches the speed of the piston in no time. Then after bottom dead center, and the piston starts charging back up, guess what? That charge of air is STILL cramming into the cylinder because it has so much inertia. Kinetic energy packing air into the cylinders increases with the square of it's velocity. And the same holds true on a turbo motor.
You choose where you want your torque to peak and then do the math to figure out what the cross sectional area needs to be in order to reach peak velocity at that given rpm. But a pretty small runner can peak torque at a pretty high rpm. You can flow alot more air through a small port than people think. The key is to gain flow from everything EXCEPT enlarging the runner. Enlarging it is a last resort, reserved for when optimizing port design no longer gains you anything in the rpm range you're playing at. And there are many many ways to do it, but with 99% of backyard porters, enlarging the runners is the FIRST thing and usually only thing they do.