The Y-DNA Test (to my understanding) will confirm a family line travelling back up through the paternal name (Son to father, to grandfather, to g-grandfather, and so on) for a number of generations. If I understand it correctly, where you will "intersect" with cousins through this test would be where the two of you match on a common relative. So for example, if you share a g-g-grandfather Isaacs, you would find that you have a match at that relative, and would be able to genetically tell that this was a common ancestor. If you don't have your line traced back this far (again, for example) and you encounter a match like this, it can confirm or at least lead you in the direction towards this common relative. At which point you might decide to dig deeper into finding sources that would confirm that this was your common relative.
So it's all about finding your matches.