Seting up IIS5.0

When setting up a web server using Microsoft IIS, I prefer to install wwwroot directory and FTP in a different drive other than C. unfortunately IIS5.0 will not allowed you to change the setting and will install everything in drive C. how safe that is and is there a way to install FTP and wwwroot in another directory when setting up IIS5.0. What is the safest practice for doing that?