For Taxonomy codes to print on the claims you need to do the following.
1) Check if the taxonomy code is entered in the system under provider information.
Login as admin / <password> - if you don't know your password then call tech support @ 630.219.1919
Go to Master Data -> Provider Information
Edit the doctors information and go to the PINS tab and enter / verify the taxonomy code
2) Check if the Insurance Master Record has "Requires Taxonomy Code for Claims checked.
When the above 2 points are configured the claims should print and send the taxonomy codes in electronic claims.