The idea behind quota is that users are forced to stay under their disk comsumption limit, taking away their ability to comsume unlimited disk space on a system.
Quota is handled on a per user or per group, per file system basis.
If there is more than one file system which a user is expected to create files, then quota must be set for each file system seperately. This may help to some that wants to limit their users. What I have done in my system may help you too. Here it is. First of all, you have to check if your kernel supports quota.