In principle the System 6000 Integrator can be used in the context of a project like any other plug-in.
However, please note the following:

The fact that you can use the System 6000 Integrator to retrieve data from a System 6000 MKII frame and send it back to the same or a different frame later gives you a powerful and flexible mechanism for using 'User Pre-sets' and 'Scenes'

Having all data in one place will give you peace of mind and free you from the necessity to store your precious settings in files or on physical media.
As you transfer data (User Pre-sets and Scenes) from a System 6000 MKII frame to your computer, these User Pre-sets and Scenes will be stored as part of that particular instance of the plug-in.
Accordingly, you need to make sure that you do not lose the project and the plug-in instance where your data is stored.

To avoid data loss in cases that you can delete by accident a System 6000 Integrator plug-in instance on a track, the track holding the System 6000 Integrator plug-in instance or the DAW/NLE project with that track and plug-in instance,  effectively  you will lose the data stored in this plug-in instance.

Please make sure that plug-in instances in projects containing valuable User Pre-sets and Scenes are not deleted.

When you do “house-cleaning” in a complex project, never delete tracks that only contain System 6000 Integrator plug-in instances or otherwise  will look empty.

It is good practice to incorporate the plug-in on a track in your project that cannot easily be deleted.

For example, you could create one track called “System 6000 MKII” and insert one or multiple plug-in instances on this track.