Hope I have understood your question correctly:
1. Save your existing non-Pro Matrices and Presets if that is not already done.
2. Close your existing non-Pro instances (optional, but probably helpful to avoid clutter).
3. Open a new VI-Pro instance.
4. Load a saved Matrix or Preset.
If you haven't worked before with saving your own matrices and presets, I suggest you first experiment with it on a small scale before doing it systematically. Learn how to create subfolders. That way you can figure out a helpful folder organization and naming convention. Time, thought and planning invested in this step will pay dividends down the road.
For example, I'm a stickler for organizing my matrices and presets in score order, so I developed a score-order folder and instrument numbering system to prefix to the file names. That way they are automaticallyl sorted in score order. Main folders could be named 1 Winds, 2 Brass, 3 Percussion, 4 Keys-Mallets, 5 Strings. Then under 1 Winds you could use something like 1 Flutes, 2 Oboes, 3 Clarinets, 4 Bassoons. You could then name the actual Flute instrument presets as: 1 Piccolo, 2 Flute 1, 3 Flute 2, 4 Alto Flute, 5 Bass Flute, and so on. This is a simplified version of what I do. I also systematically add letters to the end of instruments to add a separate preset for mutes (1 Brass / 1 Trumpets / 2 C Trumpet-m) or ensembles (1 Winds / 3 Clarinets / 1 Clarinets-a3).
By the way, if you change your mind on how to name your newly saved files, you might also want to experiment (on a small scale first) with renaming them directly in the file browser of your computer. You can find the files in your VSL Custom Data folder. This will save you a TON of time over using the clunky interface in VI Pro.