This will cause prblems with suexec, as suexec will refuse to work on all new websites. I highly recommend to change that back. Instead you should configure quota for / and /home partition in /etc/fstab and then run The resync tool (Tools > resync) for all websites.
I did what you told me, it looks OK now, I can see the used space and the soft/hard limit Thank you till. Do you know if it's possible to disable website's backup for a customer ? And to limit a size for a mysql database ? Cause I wasn't able to find those options on ISP Config nor in the manual
Mysql quotas will be availbale in ispconfig 3.1 (are already implemented in git). The backups can not be limited yet. I will add a feature request in the bugtracker.