Congrats on the new job!
From time to time I have to manage sites like this where you come into it after it has been poked and prodded for years. It is hard making changes because you are not sure what you are going to break.
My #1 suggestion would be, setup a test machine somewhere. I have a couple of old PC's that I have installed LAMP (linux, apache, mysql, php) on and use for testing. Basically copy the production site to your test server and make your changes there first before rolling it out on the production system.
This can save you HOURS of headache.