What exceptions did you mean? Did you mean you want to use this Better WP Security on your site that thas W3 Total Cache installed?
I’m using both Better WP Security and W3 Total Cache on my website, it’s working correctly, no any additional configuration needed.
Some suggestion:
1. Make necessary backup, both files and database.
2. Also make backup of theses files: .htaccess, wp-settings.php. In most cases, if Better WP Security breaks your site, simply copy/paste those files from backups can restore your website.
3. Make sure you have installed W3 Total Cache and your website is working correctly before install Better WP Security. After installing Better WP Security, you need to empty all caches.
4. Many features in Better WP Security could breaks your website because high memory demand, incompatibility issues with your webhost, etc. So it is good to enable one-by-one and test it before you enable another new feature.
5. These features are frequently reported has problems and have high potential to cause your website not working: Enable Away Mode, Change wp-content directory, Enable Scheduled Backups, Change Database Prefix, SSL.
6. You should read the information provided before you enable anything in the plugin. Don’t eanble it if you don’t understand.