Sorry to hear about the recent issues you have been experiencing.
You would need to have two separate tracks. One audio track for the recorded guitar, and an instrument track for Presence. After you record MIDI on the instrument track, double-click the MIDI event to see the MIDI Editor. Here, you can see the notes being used.
As the Answers system is not designed for back and forth conversations, please create a support ticket if you would like to discuss this in more detail.
Here is a link to create a ticket: http://support.presonus.com/hc/en-us/requests/new