1) Click the 'File Structure' tab:

2) By default, 'Full Path' is selected for new themes.  A description of each type of Directory Structure appears below the 'Website Directory Structure Preference' field.

Basically, the radio-button selected here determines how your Silo index pages are named and whether a separate directory is created for each Silo of your site.

The only difference between these choices is how long the URL's for the different pages of your site become.  If you have very long keyword phrases for your Silos and Articles, you may want to choose either the 'Virtual' or 'Hybrid' preference.

For most sites, the default 'Full Path' will work fine.

*Note:  If you change this selection after adding Silos and Articles and/or uploading pages of your site, you will need to drill-down again into each Silo and Article so that the proper URL's will be re-created, and then you will need to upload the entire site again for the changes to take place.

3) By default, '.html' is selected for new themes.  Choose a different File Extension Preference by clicking on one of the other radio-buttons.  If you don't see the one you need listed, click on the 'Other...' radio button and enter the file extension you want:

*Note:  Be sure the first character of your own File Extension Preference is a '.' (period) or your files will not be created with a working File Extension