The default setting for a FAF event does add the registration fee to the Fundraising totals, so no change is needed if this is a new event, or if you have never changed this behavior. 

If you wish to disable this behavior
  1. Go to Communities > Special Events > Friends Asking Friends > Kintera Thon >
  2. Hover over the event name and click Website Info
  3. Click Website Features under Event Customization
  4. Under Participation Registration section, check Do not add registration fee to donation totals
  5. Scroll down and click Save
  6. Go back to the Website Info and click Update Your Event Now

Turning it back on is as simple as following the steps above, but in Step 4, uncheck the box. The continue with Step 5 and 6.