I've seen cases with small exhaust vents in the rear, small intake vents in the front, and a huge intake fan on the side panel. Fans are pulling more air in than they are pushing out. That doesn't seem intuitive to me.
Shouldn't the fans be arranged so that the air intake equals the air outtake? (ie One big intake fan on the side panel, an all the other smaller panels for exhaust).
You are somewhat over thinking the issue here. Usually there it at least 1 80mm exhaust fan on the back of the case along with the fan in the power supply (which now aday's is usually a 120mm fan). On the from is either a 80mm, 92mm, or 120mm fan. And the fan on the side ofthe case can be anywhere from an 80mm fan to a huge behemouth 240mm fan.
Now IMHO it is best to have more exhaust than intake since you want more air movement to get heat out of the case. But that is why alot of cases also have a "blow hole" fan on the top to get even more hot air out of the case. I usually recommend the following:
1x120mm on the front of the case and 1x92mm on the side of the case for intake
and the following for exhaust:
1x120mm on the back of the case, 1x120mm in the top of the case for a blow hole, and the psu fan.
I have used this setup on my current server rig for just under 2 years and it works like a charm.
Almost, the over all air moved will be equal your right; but it may occur at (in this case) a larger surface area for the intake and output at a faster rate. Just like in fluid dynamics. So the over all amount of air moved is equal.
If the supply fans suck in more air than than the other fans exhaust then the extra air will go out thru the vent holes. Some of the extra may actually "boost" the CFM of the exhaust fans and go out that way.
As long as the fans are close to being matched (CFM not mm) then there should be problems as long as there is enough air moving thru the case.