After you install Conga Orchestrate, you can either configure security via Permission Sets, Profiles, or a combination of both. If you already followed the Permission Sets directions, it is up to you whether you desire to configure your profiles.
To configure Profiles follow the steps for End User Security access and Administrator Security. An End User executes or participates in a process. An Administrator creates process definitions. Whether you chose to Grant Access to All Users or Grant Access to Administrators when installing Conga Orchestrate, configure your security profiles to match. Apply these changes to the appropriate custom profiles in your organization.
When you upgrade Conga Orchestrate, your security settings will not be overridden. Therefore, it is safe to choose Grant Access to All Users when upgrading Conga Orchestrate.