I am located in Georgia USA, I get a list by County from the dept of revenue showing what sales tax to charge.
In Commerce we need to define by Zip code. After looking around i got a list of Zip code by county and everything worked out fine except one problem. There are some zips that appeared in two different counties. I found that some street addresses belong to one county and some to other in the same zip. Is anyone else facing a same problem?

I asked that if they provide an address lookup service which when address is passed, returns a county. They said no they don;t provide that. This will be very helpful to get the right tax rate. I hope they include this in the new version 4.0 "Defining Sales Tax by County with address lookup".

Any suggestions, How are other s doing it?

I dont' know of a solution to the situation in which a zip code crosses county borders. However, you might want to call the state again. Every state is different, but I suspect you got an answer to a question you did not ask.

In most states you have to charge the tax rate that is in effect in the place you are doing business. If you do business in Augusta, GA, you charge Augusta's tax rate, even if you are selling to someone in Atlanta.

This is what I do in Arizona. Doesn't matter were I sell to in Arizona I have to charge the tax that the business is loacted in.

I would make the call...they will tell you the right way!

I will make a call to the revenue dept but in Georgia when i went to buy a refridgeretor to Sears they charged me a sales tax based on my shipping address which was less than the rate where this store was located.
Just an FYI....
Any other suggestions are welcome.

Sears may have done that because they have many locations. I think if you only have the one location then you would only charge sales tax required for that location.
I am also in Arizona and we only need to charge sales tax to customers that are in Arizona. If we ship something to another state then we don't need to charge tax.

Larger companies with multiple locations will need to charge sales tax if they have a store in the same state as the goods are delivered to.