When installing a component from the command line, you can apply properties to specify the component's installation settings.
For example, to change where component files are installed, apply the component's directory property. For the server-side Signature Deficiencies for Epic files, the directory property is APPLICATIONSERVER_FILES:
msiexec /i "Hyland Integration for Epic.msi" ADDLOCAL=SignatureDeficienciesServer APPLICATIONSERVER_FILES="C:\inetpub\wwwroot\DMSAppServer\" /quiet
For a complete list of properties for each component, see the Features & Properties Reference for Command Line Installations.