Ok, I wasn't following what you were describing; now I get it.
I'm pretty sure my mac came with an Applications folder in the user account folder and I would like to get it back that way. Is there any way to do that without having it be a copy, and get back to this original state?
Like Gregg2 said, unless someone else set the computer up for you, there isn't an Applications folder in your user folder by default. You either created it without realizing it, or someone did it for you.
There are two possibilities:
1) There was an alias of the main Applications folder in your home folder; this means that while you could click on that file to show the contents of Applications, the actual files are stored where they're supposed to be, at the top level of the hard drive--it's just a pointer. The icon would have had a little black arrow in the corner if this was the case.
To recreate such a link, just drag the Applications folder to where you want the link while holding down the Command and Option keys--the dragging arrow should show a little black curved arrow on top of it to let you know that you're going to create an alias.
2) There was, indeed, an Applications folder in there. A few people--usually relatively tech-savvy ones--like to have some of their applications just installed for that particular user, in which case they create an Applications folder in the user folder. A handful of specific apps also do this (the only one I'm familiar with personally is Crossover, which creates an Applications folder in your home folder that contains a link for each Windows app installed).
If one or the other of these were the case, that Applications folder would only have had a few things in it, and if it got deleted, everything in it would have also gone with it.
It doesn't sound to me like #2 is your case, so I'm guessing an alias--recreate it as described above and see if this does what you were looking for.