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From what I can gather you are having some difficulty with the bookkeeping associated with the sales taxes and shipping and handling expenses.
Until your organization receives its IRS tax free designation (501 derivative) you will not only have to charge sales taxes but also pay taxes as an organization on revenue generated from sales.
One way to deal with the accounting aspect is to set up separate general ledger accounts for sales taxes and S&H charges, book sales taxes as a business expense and charge S&H as part of the product cost of sales. These accounts would then reside in the customer ordering system and map the expense and cost of sales to the general ledger.
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