You asked: "Is there a way I can flag the Source/Citation to indicate that I have an original copy on my computer?
This is what I do:
1) Select one of the citations for this source (people screen, right side) and double click on it.
2) Select Media tab - third from right
3) Select "ATTACH Media" (note: NOT Link Media)
4) Browse to wherever you have this media item on your hard disk (media can include text, word, pdf, jpg, html, etc.)
5) Check the box for what category it is, ie death certificate, etc.
6) Click ok.
Now... notice that an icon will appear for duplicate of that citation - it kind of looks like a brown camera.
That icon is the visual signal that you have the item in your FTM Media folder and you can look at it by double clicking on the citation, then double click the image, then if you wish you can click on the "edit" screen to bring it up in another program. (ie word in excel, text in notepad, jpg in Windows Photo Gallery, whatever.)
Note that I strongly suggest you always ATTACH the media to the citation - which makes a copy from wherever it is in your hard disk and places it in your FTM Media Folder. As time goes on and you want to move your FTM files to a new computer, or you decide to clean up your documents folder, you may inadvertently move stuff and FTM won't find it when you need it - if you use the link option.
This is also how you can move your paper copies of docs into your FTM file via a scanner.