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I am logged in as user "vlado" on my MacBook running El Capitan. If I go and type whoami in Terminal, it says vlado too. So this is fine. But in my folder structure in hd/Users/vlado/Applications I don't see my Applications, which I can otherwise see through Finder. I have my applications no problem and I run them no problem, but the folder structure is confusing me. Shouldn't the applications go into my user's (vlado's) folder structure and not to hd/Applications?

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Just a quick answer....

Items in the Applications are system wide, not per user. You can deny Users access to particular applications, but in general they are available to everyone.

The User folder holds items that are specific to each user and only available to each user individually and the superuser (root).

Macworld has a good article that goes into this further

Also, OS X Daily had a nice summary table of the folder structure which should be helpful:

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