Personally I'd always opt for the Java installer over the repo/deb installation because installing it yourself gives you much more flexibility, for example if you want to sidegrade from I2P to I2P+, or if you want to test development builds, in addition to having all your configuration files in a single location (as mentioned).

You can stop the I2P service and try out the java installer if you don't want to fully commit before you've got comfortable. You could always try the I2P+ installer, details at: http://skank.i2p

Back to your original question, given you're currently running a repo installation, and you appear to be editing files in the correct location, the only thing I can think of that may be causing issues is your browser cache retaining the default index.html file which redirects to /help. You can test this theory by creating a separate file in docroot/ and browsing directly to that instead, e.g. testpage.html .. if this works, clear your browser cache and try accessing the site again. And be mindful of the file permissions on any new files you create.