Is this cron supposed to run as root, or is it just a "user" cron?
Generally you don't enable cron jobs by FTP, but I suppose it is possible, if you give the FTP user access to the actual crontab file, but that is generally considered "bad Unix" since it opens up all sorts of potential security problems.
These sorts of jobs should really be done from an SSH command line in the system, with a program called. I wouldn't even recommend doing them with regular Telnet. Also, users don't even usually have read/write access to their own cron files, but must use the "crontab" utility (not /etc/crontab) which will take their input and create the appropriate file at /var/cron/tabs.
If you really need remote access to manage these sorts of things, and you don't want to use SSH, I recommend installing Webmin (it's in the FreeBSD ports at /usr/ports/sysutils/webmin). Webmin gives you a special SSL webserver at port 10000 (or any other non-standard port) with an amazingly complete system administration utility. It's not as good as learning to do the real command-line stuff, but it's definitely better than trying to configure your system with FTP.
As to the actual details of running cron, I recommend checking out the following link:
Actually, this site has some great tutorials on FreeBSD in general, including Webmin:
As to your second question, again it's one of those things that is changed from the command line. I doubt any sysadmin normally thinks about where the actual information to set the system time is, since it is never set "by hand". The "date" utility is the program to use here. Allowing the non-root FTP user to access such sensitive system files as this can also open up some potential security problems. If a hacker can easily change your system time, that can wreak havoc on whatever serious software or web app you are running.
May I ask what all this pertains to? I have never heard of anyone trying to change such things with FTP. Maybe you need to do some research into network programming, and remote procedure calls, etc...
