Linear algebra, maybe a little calculus, and a lot of testing.
There's no real mystery to this sort of thing, but people often just don't think about it in the rigorous terms you need to get a system that is fairly well-balanced.
Basically the designers know how quickly you can gather resources (both the best case and the average case), and they know how long it takes to build a unit, and they know roughly how powerful a unit is (eg. by reference to approximations such as damage per second). With this, you can ensure a unit's cost in resources makes sense. And from that, it's possible to compare resource gathering with unit cost to model the strength of a force growing over time. Similarly you can measure a force's capacity for damage over time, and compare the two. If there's a big disparity then they can tweak one or more of the variables to reduce it. Obviously there are many permutations of units but the interesting thing is that you only really need to understand the most powerful permutations - if a player picks a poor combination then it's ok if they lose. You don't want every approach to be equally good, as that would imply a boring game where your decisions are meaningless.
This is, of course, a simplification, but it helps get everything in roughly the right place and ensure that there are no units that are useless. Then testing can hammer down the rough edges and find most of the exploits that remain.