Always make a backup of your database before upgrading!
The easiest way to upgrade the Emilda source is probably to move the old directory to a backup location, install the new source from the tarball and copy over required files from the old installation. Here's an example:
mv emilda emilda-1.2-alpha tar -zxf emilda-1.2-beta.tar.gz mv emilda-1.2-alpha/src emilda cp emilda-1.2-alpha/config emilda/ cp -a emilda-1.2-alpha/perl/barcodes/* emilda/perl/barcodes/
Also copy/move over any other files/directories you may have in the old emilda dir that didn't come with the original tarball. If you have the Zebra database in the emilda-1.1 directory, move it to the new emilda directory.
Now point your Internet browser to http://your-old-emilda-address/setup.php and follow the on-screen instructions. After a successful setup your Emilda database will have been converted to the right version. You may want to disallow access to setup.php after completing the installation, although, nothing harmful can be done with it after a successfull installation.