There are several options.
The simplest way is to wait for the packagers to catch up and provide the program in synaptic. Then you just uninstall the software from source (make uninstall) and install the package from synaptic again. This is what most people do.
The 2nd simplest way is to download the newer tarball, uninstall and reinstall. This is what some people do.
The 3rd way is to use git or svn to sync with the source from the developer's repo, and use make to recompile only what have changed. This is supposedly faster than reinstalling from scratch, supposing you do it often. Very few people do it.