Mission Control handles window selection and visualization. Open that preference pane and look at the Application Windows keyboard shortcut.
Control down arrow (or in the trackpad preferences enable App Exposé - three finger swipe down) to activate the picker.
From there you can select a window or arrow key left right to the window you desire.
- command + [ or ] will switch to the next / previous window
- command + { or } will switch to the next / previous tab within a window
Some applications - terminal is a notable one - define menu items to select the next window in turn. If they do, you can usually override the keyboard shortcut if you don't like the ones they chose by default.
Apple's window manager isn't a perfect fit for the design idiom of windows, but in this case, it's pretty close once you re-train your expectations to having all the windows one tap away.