Where Do My Applications Live?

Hello
I was wondering and this may be a stupid question so please forgive my ignorance.In my sidebar I having showing in this order: Applications. Desktop. Documents. Downloads. Music. And my home folder named Jaco. Devices I have the Mac HD showing which I also named Jaco. So today I was going through the sidebar and under my home Jaco directory I only see three third party apps that I installed, unless that's where the install by default. All of my other apps third party and Mac apps show in the listing in my side bar Applications. When I open that folder I see all but the three apps I mentioned above. And the Mac HD is highlighted. So if I double click and open that under Application that's where I see my apps, Is this how the direcrtory structure should be?
Thanks. Any help and advice to make this clear to me is very much appreciated.
Regards,
MacJosepg

Here is my Home Folder for comaprision:

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