The TIMS3 Preferences dialog accessible from the main Application pull-down menu, allows you to set certain controls that affect the behavior of MicroStation.

The Confirm Actions controls whether you are prompted for confirmation for any of the TIMS3 operations within MicroStation.
The Compress File on Exit will perform an automatic MicroStation compress operation when a file is closed, i.e. when you exit MicroStation, or when you open a new file.
The Resolve Reference Paths will instruct the TIMS3 system to examine reference file attachment names and create the required MicroStation configuration variables as needed to define local pathnames for "project logical" prefixes.
The Force Ref Logical Attachment option will ensure that a TIMS3 "project logical" prefix is appended to a reference file that is in the same project/directory as the master file. Normally, only reference files form a different project will have a "project logical" prefix. The usefulness of having a "project logical" prefix placed on local file attachments is so that the master file may be copied to another project and a link to the reference files in the project is maintained, otherwise all local references would also need to be copied to the new project.