How do I get these folders to sync up?

Is there a application or something?

kalvinandhobbes8,
YIKES! Why do you have (almost) your entire "Applications" folder duplicated within your HOME folder? Did you accidentally copy it there, or did you intend to do this for some reason?
My recommendation would be to place the copy that resides in your HOME folder in the trash, then empty it. You will recover a great deal of disk space by doing so. There may be some complications in removing that folder, though; you may have some of those duplicated apps running, or you may have some of them linked in your Dock. You might even have some applications that exist in that extra folder in unique versions.
So, you'll want to go through that extra folder and pull out any apps that either only exist there, or exist in version that you wish to keep. Place them in your real "Applications" folder. Then, quit any running apps, place the extra folder in the trash, and try to empty it. If you end up with "question mark" icons in your Dock, just drag these icons out of the Dock. You can replace them with the same apps from the real "Applications" folder.
Scott

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