Don't worry if you don't know how to init 3. You should just be able to sign on as root and type the command xf86config. I'm pretty sure that xf86config doesn't require an X session so it shouldn't matter what level (3 or 5) you use in this particular case.
just keep your settings simple (you can refer to http://www.luv.asn.au/overheads/xconfig/
for some ideas. After you get a rudimentary s session going, you can xf86cfg or use Xconfigurator to fine tune. Also, if you are hung up on a particular problem (i.e., a mouse issue), there are commands specifically for those issues (e.g. mouseconfig) which may be helpful.