How to move WHMCS to a different directory
1. Remove anything that may conflict with WHMCS from your public_html directory
2. Login to your admin panel and change the system URL to http://www.yourdomain.com/directory/ (http://www.yourdomain.com/ for root) under setup > general settings > general > system location
3. Move your files from inside your folder to the directory of your choice directory (File Manager in cPanel makes this easy)
4. Re-issue your WHMCS and enter the new license code when it’s requested when you go to login to your admin panel
5. Delete & re-add any WHMCS related Cron jobs you have running. Most users will have the WHMCS automation cron setup (setup > automation settings). In most cases there is a cron job for domain registrars also.