1. Click on the Tools menu > Options
2. Choose Files in the Indexing list on the left
3. Click the Select Files to Scan... button to launch the Files Indexing Options menu
4. The key in the right hand pane details how to select the folders in the left pane for either complete, partial or no indexing
5. When you've completed your selections click "Ok" twice to close the Options menu.
The next time X1 indexes your files, the selected folders will be added or removed from your index (depending, of course, on what you chose).
For example: to perform an index update of your files, click on Tools > Options > Files and click on "Index Files Now".