The key to why a window will cover the taskbar is because you have the properties of an app (or apps) set to run full screen. You should set to "normal window". You can then open any app (or apps) and drag the edges of the window to whatever size you want. If you want an app to use all the screen space, drag edges until it's a few pixels shy of full screen.
Windows will remember whatever size you make it.
Remember, if you use the snap feature, to always snap windows back to their normal size before closing the app..
Doing it this way allows you to auto hide the taskbar if you wish and the windows won't cover it up.