The user that is used to install the Analyze instance on the Widows Server machine will require full access to the installation directory. Similarly, full access will be required for the directory specified to hold the 'site' configuration information and the 'data' directory storing the intermediate data generated by the operation of the system.
When users access the Analyze system UI via the browser, all operations are performed with the privileges of the service account under which the Analyze software is running, not the identity of the end user accessing the system. However, when running a data flow that access is configured to access an external system or service, for instance, a database or SalesForce, the nodes are typically configured with the credentials of the individual user. Credentials can be specified using Run Properties - allowing a common data flow to be used by multiple individuals but require the user to enter their credentials at run time (or when the schedule is created). Where the system is set to store a password this is securely stored in an encrypted form.