I'm not sure, but I also think that aligning Hex Maps is a bit of a bother, especially for larger ones. I tried following the advice you gave above Gauss, but I'm kind of not sure I'm following them correctly. Do you have anything like a set of screenshots, or better yet, a video, that shows how to most easily align a Hex Map? That would be great. Right now I'm spending quite a bit of time trying to fidget it into place, and it's just not quite working, even with the use of the ALT key, and trying to pull the scale bars around, as well as trying to use the Align Map feature.
For future reference, while I don't disagree with JonathanTheBlack in terms of "Yup, this could be a little easier", I think my solution would be to offer the user the ability to select "Grid Map" or "Hex Map", and allow the person to point and click the Polygon to its actual size (rather than trying to drag "Three Units" which on a hex map happens to be a bit confusing so far as instructions go), and THEN allow the user to fix the final result by setting the exact values in a dialog box as JonathanTheBlack suggests. Between those two, it should meet everyone's needs. Quick and efficient scaling of imported maps is kind of an important feature since the entire purpose of the tool is to use maps and be able to effectively move tokens around on it. If we have to futz around with it, it takes valuable time away from other more productive aspects of GMing setup... *especially* if you are trying to do this spontaneously during the game. Anyway, just my two cents... and over all I give roll20 a huge and friendly slap on the back - Job well done! Thanks!!! It really is awesome!