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 invoice software for United States businesses  invoiceit!
NY County Tax option
overview

this option allows automatic NY county tax based on customer's location and provides tax reports by county, both tax collected (based on receipts) and tax charged (based on invoices). 
It can also be used in other states where you are required to apply county or city taxes. It has a large database of all zip codes and their associated counties, throughout the US and dependencies.
1) after you have purchased and downloaded the option, install it, then click on Setup - Network button and connect to the county database 
2) on Setup p.1 - select your state from the dropdown and click Yes for the County Tax option.

Where state and county tax is combined (as in New York state), set state tax rate to 0. The county tax rate shown is a nominal rate only (it must be greater than 0). However, the actual rate will be that of the customer's county to which you made the sale.

3) click button 'County List' and enter the tax rate for each of the counties that apply them. Flag those with exceptions and explain them so your operator knows what to enter when this county comes up on invoice.
Setup is now complete
when you set up customers, check the tax that applies to them. If they are out-of-state or overseas, uncheck the box and no tax will be applied.

Where shipping addresses are used, the tax is applied depending on the location of shipping address.

products, inventory and service charges - if you supply an item that is NOT TAXED, set the tax rate of that item to 0. Otherwise do nothing.
Rate shown is nominal. Actual rate will be that of the customer's county to which you made the sale.

Rate is shown at lower right of picture -->

When you select the customer on the invoice, the county name and county tax rate will be set on the invoice (center right in picture). Click Map button to view a map of the zip code area (from ship to address or, if not shown, from bill to address). Map requires internet connection.

When you add a charge item to the invoice, the program checks the following:
a) is customer taxable
b) is product/service taxable
c) is US County tax option enabled

If all three are true, the tax is calculated at the rate shown in county tax rate.

You can edit taxes easily with Taxes button at lower left of invoice input form (also on quotes and auto-invoices)

Reports are available that give you the option to print out either tax collected (based on payment receipts) or tax charged (based on invoices). 

Here is an example, based on invoices.

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