I’m not sure if this is the default behavior, but when I open multiple windows, I get multiple status bars (see below). This is ideal when I have multiple windows open. However, when I try to search, or issue a command, it goes all the way down to the bottom (see below). Is there any way to force it to show in, over or under the status bar of each window?

I think you are confusing status-line and command-line. Type:
and:
There’s no way to move command-line somewhere else, unfortunately, nor combine these two. You can even turn the status line for “last” window (the bottom ones) by using:
just to emphasize the difference.