When installing Kentico there are two things you install:
1. Kentico's toolset i.e.: Kentico Installation Manager (KIM), Kentico Import Toolkit (KIT), installation files for any new websites you add, etc. These are used to manage your website(s) from a high level.
2. The option to install a website. If you choose to install, choose a custom installation and choose NOT to install a demo site by selecting a Blank Website (Portal).
Now this being said, you will have 3 main directories in which you have files on your system:
A. C:\Program Files (x86)\Kentico - holds the Kentico files, I mentioned above in #1.
B. C:\ProgramData\KIM - holds all of the upgrade and hotfix info for your websites you manage within the KIM.
C. C:\inetpub\wwwroot - this directory would be the root of your website(s) but I choose to place mine on a different drive so all my projects are off of my OS drive. Typically this is pretty common place.
So to clarify a bit, you will have a bunch of tools which allow you to manage your Kentico websites (A and B above) and then you will have your websites themselves (C above).
Needless to say, the files in your wwwroot directory NEED to be there if you decide you want a website. As I mentioned, you can install your website in any location on your drive, you just have to make sure IIS is pointing to that location and IIS has proper access to the file system.
If you haven't already, check out the Installation Guide. The documentation is very good and should be able to get you going pretty quick. If not, look me up and I'll work with you to get you going.