Yes, you would want to uninstall emacs before installing it from source.

sudo apt-get remove emacs

That should do the trick.

If they do not provide an uninstall script (usually made when you do a make/make install) in the source folder, you are pretty much out of luck for uninstalling cleanly, unless you can figure out what all it installed and where.

I looked and couldn't find a current emacs repository, which makes install/uninstall much safer. In general, don't install outside of repos (or at the very least .debs), unless it is something you really need, just because it can be so messy.