does iweb use it for anything important.
The domain file
IS your site. Everything iWeb uses to create the site when it publishes it is in the domain file. Photos that you add to the site are copied into the domain file. You lose it and you lose the site so be sure to have a current backup of the site, i.e. after every change you make.
You could use an HTML editor to modify a published iWeb page but there is a chance you could mess up the page since iWeb uses javascript a lot in it's creation. Also iWeb wouldn't know about the changes and will overwrite them if you use iWeb to make additional changes. So the answer is yes but don't do it.
If SEO is working for you then go ahead and continue. Just be on the lookout for problems and if they come up give Cyberduck a chance.
If you startup problems are occuring when you boot into OS X try booting into
Safe Mode, shut down and reboot normally. See if that will help. Safe Boot will run repair scripts during it's process and might fix what's causing the problem. If that doesn't help ask in the
Mac OS X v10.6 Snow Leopard or
iMac forums.