The 1099 and 1096 functionality has not changed from previous versions. It is still a multi-step process that has the end result of printing the information on blank pre-printed forms. What has changed with Version 2006 is that the 4 of our 6 recommended steps are now organized on a new wizard.
To process the forms from QuickBooks, complete the steps detailed below.
Step 1 – Confirm Payees are Vendors and set up properly
Step 2 – Confirm Vendor Tax ID #
Step 3 – Edit the 1099 Company Preference
Step 4 – Prepare Reports
Step 5 – Confirm Business Information
Step 6 – Print the forms
New with version 2006 is a navigator to aid in the process of steps 2, 3, 4, and 6. Step 1 and Step 5 will still need to be completed without the aid of the wizard.
QBRA-2006: Vendors > Print 1099s/1096

Confirm that all payees that will require a Form 1099 are on the Vendor list (Lists > Vendors List).
If there are any names on the Other List (Lists > Other Names List), single click on the name, choose Other Names > Edit > Change Type > Vendor > OK. This activity will move the name and related transactions to the vendor list.
If a customer name has been used (Lists > Customer:Job List), a new vendor needs to be created with a slightly different name (Lists > Vendors List > Vendor > New) then all transactions using the customer name will need to be corrected to use the new vendor name. Then, go back to the customer list and delete the incorrect name to ensure that the wrong one will not be chosen in the future.
Edit each vendor from the vendor list that will require a 1099 and confirm the following:
QBRA-2002: Reports > List > Vendor Phone List > Modify Report > Display Tab > add the columns for Tax ID and Eligible for 1099

To complete the paper trail, it is advised that each vendor eligible for a 1099 complete a W-9. This form can be obtained from the local IRS office, by calling 1-800-829-3676, or from their website at http://www.irs.ustreas.gov/prod/forms_pubs/forms.html.
TIP: Start this process early and double-check it regularly throughout the year. It is much easier to obtain the information as new vendors are paid, than to go back and try to accumulate the information at the end of the year.
The change with version 2006 is that there is a report already created for this purpose. By clicking on the “Run Report” button a report is generated that already has added the columns as described above. Because it is a list report, the same drill down capability is available.
QBRA-2006: Vendors > Print 1099s/1096 > Run Report

Make sure the preference has been set properly:
QBRA-2006: Edit > Preferences > Tax:1099 > Company Preferences

The change in version 2006 is that by clicking on the map accounts button, the preference automatically opens.
The 1099-MISC forms are based on a cash basis, i.e. the amount paid will be reported when the check is actually issued as opposed to when it was incurred or due. These forms are due annually, and are typically prepared in January of the subsequent year. For that reason, the default date is set for the last calendar year. As with all reports, the date can be changed. To create a report to show the individual payments included for review prior to printing the 1099-MISC forms, choose Reports > Vendors & Payables > 1099 detail. It is recommended that you retain this report for supporting purposes for the printed forms. To see the totals only, choose Reports > Vendors & Payables > 1099 Summary. To be sure no one has been missed change the choice at the top of the report to include all vendors.
QBRA-2002: Reports > Vendors & Payables > 1099 Summary

The change with version 2006, is that the report is created by clicking on the “Run Report” button on the 1099 and 1096 wizard.
Confirm that the Address and the Legal Name, as well as the Federal ID number for the company issuing the Form 1099-Misc are accurate.
QBRA-2006: Company > Company Information

Printing the forms is done through File > Print Forms > Print 1099 > Assign the date range > OK > a box then appears with a listing of all of the 1099-MISC forms to print. Note the 1096 information at the bottom, left hand side of the screen. QuickBooks does not print the 1096 form in version 2003 and prior. It only provides the information to fill in on the form. Starting with version 2004 printing the Form 1096 has been included. The number of copies of form 1099-MISC required, up to 8 parts, varies by state. At a minimum, 3 parts of the pre-printed forms are needed: one for payee, one for payer, and one for the Internal Revenue Service. Designate the number of copies to be printed at the bottom of the print screen. The pre-printed forms and corresponding envelopes are available from local office supply stores, or from www.intuitmarket.com, or by calling Intuit at 1-800-433-8810. The forms are usually available annually August through February. As of version 2006 and prior, it is not possible to print the 1099 or 1096 on blank paper.
QBRA-2006: File > Print Forms > Print 1099 > Assign the date range > OK

The change in version 2006 is that the screen to assign the date range for the forms automatically appears from the “Print 1099s” button. Once the date range is acknowledged, it is possible to print the 1099s and 1096 forms.