I've installed Winstep Nexus for a while. And I like the option that always keep dock on above windows. But sometime this option is pretty annoying, especially when I open Facebook's Messenger, the dock hides the input at all. Is there an option that allow me to toggle the dock appear and disappear anytime I need? Thank in advanced.

Lots of different ways to skin a cat.

You can make the dock reserve screen space in the Position tab of Nexus Preferences (like the MacOSX dock and the Windows taskbar does) so that maximized applications don't cover it (warning: full screen applications are not the same as maximized applications and behave differently!).

You can bump the screen edge the dock is attached to with the mouse pointer to make it hide itself - and bump the same screen edge again to make it pop up after that (Behavior tab of Nexus Preferences).

You can also assign a hotkey to make the dock hide/pop up when you press a key combination (Behavior tab -> Make sure "Activation acts as a toggle' is enabled -> Activation Settings -> Hotkey).

Hope this help!