From the new version 0.9.8.1 CentOS Web Panel has built in function to setup quota on your server.
To enable quota on your server go to CWP.admin
– in the Left Menu –> File Management –> Disk Quota Setup
and click on the quota setup
You can also setup quota manually, here are detailed instructions:
For openVZ and virtuozzo VPS servers this needs to be enabled on the main node by your hosting provider.