subdirectory redirect

I’m brand new to WordPress and just got the site running. I’m a college professor and the site is for my music classes so nothing fancy is needed.

From a lynda.com tutorial, the instructor encouraged users to put the site in a subdirectory for security reasons so I did. I had someone at my web hosting service help me change a file that would allow users to use the domain name without typing in the /sub-folder. It works fine, but she warned me that if I customize the theme very much things could go wrong. Is this a true statement? I’m planning on using a child theme so I can change things around a bit so now I’m a little nervous. I’m wondering if I should have just installed it at the top level, although my research suggests that this redirect is pretty common.

Thanks in advance,

Aaron