The easiest way to update EagleFiler is to use the Software Update command to download and install the latest version.
Alternatively, you can replace the old EagleFiler application file with the new one. That is, if EagleFiler is installed in the Applications folder, drag the new EagleFiler application icon into the Applications folder and click Replace when the Finder asks if you want to overwrite the old version. If you get an error saying that you do not have sufficient privileges, drag the old EagleFiler to the trash and empty it, and then drag the new one into the Applications folder.