My games simply use square or hex graph paper to mark basic distances. As far as where something is in a hex, I've never found a reason to care that much. My players certainly don't; they just wanna know how long 'til they're there, and if it's important, I can randomize that with a dice toss. I guess if you really needed to know where stuff is in relation to other stuff within a system, you could hex paper your hex paper. But then, to paraphrase Gaglug, is this really worth it? I might do something like that in well-traveled systems where the PCs would be adventuring a lot, but otherwise, I just go with some basic generic star chart 2-D mappin'.