You probably already figured this out, but - the original intent of the Asset Mgm Region, Site and Department fields was to provide the "Physical" location of the asset. Conceptually it goes along with the use of Region, Site, Department in the Help Desk applications assignment process. That is to say that if the asset was physically located in Boston, you probably wouldn't want someone in San Francisco to be assigned to work on it (well maybe - but you get the drift).
However, you should use it the way that will best suit your business needs. Keep in mind though that if you are using Help Desk too, you might want to keep the AM Region, Site and Department stuff conceptually the same as HD.
Good Luck