The packages that came with the distro probably have been installed in a different place to the default, for example by default apache is installed to /usr/local/apache, rather than put the config files in /etc or the bin files /usr/local/bin, so stop your distro version of apache, then try and fire the new one up by doing
Code:
/usr/local/apache/bin/apachectl start
If you want to compile apache from source rather than using your disto's package manager to update then uninstall the distro versions to keep the system a bit neater