In short ,
If you have nothing installed now, just create your new folders and point everything there with a custom install. It will be just fine.
No there will not be any issue changing the default installtion locations with non-steam games.
For example, I have Mirrors Edge (retail) installed as
The only issue is moving a games folder that is already installed.
With Mirrors Edge for example, by default is something like:
C:/Program Files (x86)/EA Games/Mirrors Edge
If you install it there, and simply move that folder to a new location (such as D:/Games/Mirrors Edge) there may be issues, because Windows thinks its at the default location.
But, if installed to a custom location from the start, all is well.
This is why I suggest if a game is already installed on the C drive, to un-install & re-install at the new location.whatever new location you choose.
So the OS knows exactly where everything is.
As far as your custom folders go, you can name them however you want. I just use D:/Steam & D:/Games (for non-steam games) to keep it simple.
But,you can name them anyway you choose.
If you want it to be something like: D:/My Super Top Secret Games/Super Secret/Keep Out ... Have at it. It'll be fine
All that matters is that Windows knows where they are.
Steams default install path for its games is usually:
C:/Program Files (x86)/Steam/steamapps/common
All that matters for Steam, is where Steam itself is installed at.:
And yes, all games through Steam will be here, the complete game.