Yup, you enter what you want to add to the base custom tune, the one you open when SF first starts.

My SFScrape application it will let you save and reload the settings you had entered for any saved tune, however these are still settings that will be added (or subtracted) from the base tune, Special Forces let you select additive timing and fuel values in ranges that are far in excess of anything you'd really need over the base tune,

 

Oh ok.

Well what happened was I modified my original tune and renamed it. So how I have 2 files. Can I delete my old one? I'd rather just have one file saved. Or do I need to keep the original one to keep getting back to it? Or everytime I want to make changes I just go back to the one I last used?

I noticed that the only thing that was saved is my computer code and my octane choice.

 

Create one tune based upon the mods you have (I.e. you answers to the "questions"), and then use that as the base tune when you play with timing, etc.

Because of lawyers you will have to reset certain things each time you create a tweaked tune--these are the EGR and traction control status, returnless f/p (for some odd reason), and any timing and fueling modifiers.

Leave the base tune unchanged and save each tweaked tune with a unique name. I generally have 3 to 5 tunes I consider "live" at any point in time.