A little more detail, I think.
Are you opening the original or the packaged version when you have trouble with the link? Did you check the box in the package dialog to include links?
I am opening the packaged file but I am a dummy and I think I figured out what I was doing. The problem seems to be the logo's I added after I packaged it and I think what I need to do is double click on the added logo's in the links file to add it and then save when I close it. Yes?
Can I ask you another question? Do you open your file in the packaged folder and then when you want to export to make a pdf do you do it all within the packaged folder?
If you add new links, you need to include them in the links folder in the package folder (and you should relink to that copy).
I'm not quite sure I understand the second part of the question. You can certainly open the packad .indd file, make sure the links are up to date, and export a PDF. You can save it in the pacakge folder, or choose a different location. It's entirely up to you.