As you are in the U.S. can't give you much practical help (I'm in the U.K.). I would suggest you have a look at the various Japanese sites and see what they have to say.
For example,
cdJapan
Quote:
Customs/Import Duties
International customers are considered importers and must comply with all laws and regulations of the country in which the orders are received. You may be subject to import duties and taxes, which may be levied once the package reaches your country. If that happens, additional charges for customs clearance must be borne by you. We cannot predict or control what these charges may be, as they vary widely from country to country. Please contact your local customs office for further information. Also, we are required to show the accurate value of the items directly on the package.
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In general, the way it works is that you order something from, say, cdJapan (e.g. you import a CD). You pay the cost of the CD along with the postage using your credit card (note: you do not pay any import duty at this point). They package the item and include on the outside a Customs Declareation (which is usually a printed label or rubber stamp) which has the value of the goods inside. When this package reaches the U.S. it is inspected by the Postal Service and depending on the value of the goods, it may or may not then have a surcharge added (i.e. the import duty). You then have to pay this surcharge before you can receive the goods from the Postal Service. At least that's how it works in the U.K.
The secret is not to order large amounts at the same time because you only pay import duty if it exceeds a certain value (in the U.K. it's $30). Very often it's worth purchasing only one item per order so to avoid paying any surcharges. It means you pay more due to postage costs but you can very often avoid any import duty.
Anyway, that applies to importing to the U.K., someone from the U.S. will have to supply the exact details of how different it is to import into America.