PSIsafe and PSIcapture do not encrypt files as a part of their storing method.
However, during transport, i.e. migration to a web-based server in PSIcapture or routing to a web location in PSIsafe, files are encrypted with SSL / HTTPS.
If a user wants to encrypt their entire volume, or specifically the repositories/configuration of SAFE or config/batch manager MDF files of capture, as well as monitored locations or batch storage locations, bitlocker or similar encryption can be used. However, keep in mind that any locations that are set to "locked" will not be usable by PSIsafe or PSIcapture. No additional user configuration changes should be necessary in a default environment.
Microsoft documents the methods for setting up SQL SSL encryption. Once this process is completed, it's just a check box on the registration page. The full walkthrough is located here:
Finally, keep in mind that encryption methods requiring specific user rights will need to be configured so that the Windows NT Authority user has full read/write permissions at all times. This may need to be accomplished using an elevated command prompt.