How can I create application folder in home folder?

Hi there,
I'm using MacBook Pro Early 2011 model with Mountain Lion (10.8.5).
I have two questions.
I recently noticed that there was an application folder in my home folder (the folder with your username), but that application folder had been empty. I remember I used to be able to access to my applications from that folder, but not anymore.
Since the folder was empty, I deleted it before doing further research. Does anyone know if this is a bad thing?
After deleting the empty application folder from the home folder, I looked up and some said the application folder in the home folder and the application folder in Macintosh HD are two different folders. I don't know what it means, but I would like to have an application folder with applications in my home folder. Is this possible? or should I just make an Alias folder and put it in my home folder?
Thank you in advance.

Thank you for the answer.
I've screwed up my computer before doing some dumb things without asking, so I was a little paranoid.

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