I was thinking of putting quotacheck commands into my boot sequence, but will this work? how could it be done, and, will it only check quotas on boot, thereby forcing me to reboot all the time?
quotacheck only needs to run occasionally. All it does it makes sure that the usage statistics it tracks in real-time are consistent with what is actually on the disk. I don't know if you can run it on a single partition; I would guess it would have to store data under /var somewhere.
But what I really wanted to advise is not to use a single partition, especially in a production system with users. I can appreciate that it is a pain to repartition a running system, but it will only be more painful later, for example, when you want to upgrade your kernel.
Erasing your setup shouldn't be a big worry. Here's what I would do in your situation:
1. If you don't have enough disk space to create a new system disk and user disk, temporarily buy more. It would only be for one month.
2. Create a new RH system disk, a new user disk, and another small system disk (Debian would be best). Edit the new RH configuration to access the user disk, and edit the small system disk configuration to access the old system disk, the new system disk, and the user disk.
3. Boot the small system disk. Create mount points and mount all the other disks (just to be safe, mount the old system disk read-only). Using tar, replace everything on the new system disk except /proc, /dev, and /home with the contents of the old system disk. Put the contents of the old /home onto the new user disk. Edit /etc/fstab on the new system disk to mount the new user disk at /home.
Now you should have two working configurations with identical systems. Boot into the new one - if something has gone terribly wrong, boot into the old one and mount the new user disk on /home (so any user activity goes to the new disk). When everything works, remove the old system disk and small system disk sometime before the month runs out. You'll get your users on a separate disk, you'll keep your current setup, and you'll never be without a working configuration.