You will need to programmatically change the report path for each instance of TestStand.
By default the report is generated by the process model entry point with which your execute you sequence. In addition, the process model also obtains your report option settings before generating your report. The report options are obtained in the Sequence Call step "Get Report Options", which calls the Get Report Options sequence in your process model. Within this sequence the parameter ReportOptions is populated with your report option values. After it is populated you can change the value of Parameters.ReportOptions.Directory using a Statment step. This directory is then used in constructing the report path. The report path is created by the Determine Report Path step in
your entry point sequence, and the value is stored in Locals.ReportFilePath.
You can change the directory within the Get Report Options sequence by either modifying the sequence directly so that the change affects all sequence executed with the process model, or you can use the ReportOptions callback. Using the ReportOptions callback involves having a specific sequence in your test sequence (not process model) that allows you to modify the report options just for the test sequence that contains the callback. The user manual describes callbacks or you can post again for additional information about callbacks.