Sometimes the equipment profile system can present a conceptual challenge to new users. It is not immediately clear how profiles work or what happens when you change one. This section will attempt to explain how one should go about using equipment / user profiles.
First, conceptually, you should vire the profile system like you would view a template document for Microsoft Word. If you are not familiar with this concept, it basically allows you to load a Word template (like a form). Then when you fill that form out it is saved as a separate Word document... it does not update the Word template. Also, when updating that Word template, it does not change the state of any documents that have been created using that template. So... to draw parallels, a profile in SGPro is like a Word Template. When you make a sequence with the profile (like making a Word document with a template), it will use all the profile's settings as a starting point. If you further modify settings on the sequence (change text in the Word template) and save it, this will have no effect whatsoever on the profile. Likewise if you alter a profile, it will have no effect on any sequences that were created using that profile as a starting point. Profiles and targets are loosely related, but are in no way connected to each other after the initial sequence is created from it.
If I have a sequence ready and I open the PM, change some setting, and save them (e.g. auto-focus settings) how does this affect the Sequence settings and the settings found on the Control Panel?
At that point the PM does not change the sequence AT ALL. Think of the PM like a Word template. When you create a new Word document based on a template, that new document stands on it's own and will not be changed if you change the Word template. In the same way, when you create a new sequence based on a profile, the new sequence will stand on it's own. Changes made to the profile will not affect current sequences. Only NEW sequences based on a profile will include changes to the profile.
If I change settings in the Control Panel (e.g. auto-focus settings), how does this affect the Equipment Profile settings and the Sequence settings?
Changing something in the control panel only affects things in THAT sequence, it does not change anything in a profile.
I have tried changing the settings (and saving them) in the Equipment Profile Manager, but these changes were not reflected in the Control Panel. Why? Are these changes taken into account by the Sequence?
See answer to the first question. Also, if you make changes to an equipment profile, you can go to the file menu and choose to apply (or re-apply) a profile to the current sequence.
In the end, what manages/directs the Sequence? The settings in the Control Panel or the Equipment Profile Manager?
A profile will never run a sequence... it just delivers settings to a sequence. Once a sequence has been created (from a profile), at that point it is just the settings in the control panel that matter.