Press Alt+S and then V and then E to get to the Edit Verifier Information dialog box.
Alternately, select Settings> Accessibility Interview> Edit Verifiers.
Select the plus sign for Insert Record.

Enter new verifier name.

Click on the check mark to post edit.

Press Alt+F and then R and then S to get to the Setup Wizard start screen.
Alternately, select File> Run> Setup Wizard.
Select the Section 508 Report Mode (US Only) radio button, the hit return or the Next button.

In the Graph Support Mode screen select the Summary Only radio button. This makes the database smaller but still gives “executive overview” graphs. Then hit return or click the Next button.

Turn AccVerify Project Mode on by selecting that radio button. Then click on the Interview Wizard Settings… button.

In the Questions tab, Select All questions.

In the Default Answers tab, copy the following settings.

In the Process tab select the Use selected Verifier radio button.
Choose the verifier and select the Interview for the current page radio button.

In the Workflow tab select the Use Section 508 Wizard radio button, and check Run Interview Wizard immediately, Use data from previous interview, and Publish Reports when interview is complete. Then click the Save button.

Click Finish in the AccVerify Setup Wizard dialog box.

Click yes in the Confirm dialog box.

Press Alt+S and then A.
Alternately, select Settings> Accessibility Rule Settings…

This is the Accessibility Rule Settings – Section 508 Mode window.

Scroll down to Checkpoint 6.3.
Check 6.3.3, check 6.3.8, and enter the following text in the Specified Text field:
.pdf+Adobe;zip+winzip;doc+word;xls+excel;ppt+powerpoint

Scroll to the bottom of the window and check Non W3C, (n).1 – Ensure form controls are accessible for use with assistive technology.

Click OK and the rule changes have been saved.

Do not enable search for text only pages, AKA the text ghetto. This is a highly discouraged practice.
Do not check for an accessibility policy. If using the template system a link has been provided to the Accessibility page.
Do not check for Skip Navigation, since not every page needs it.