Well, it's hard to know what you did, exactly, but I've just opened K3b and will tell you the various ways I see to move the internal windows around.
First, go to the Settings menu and make sure that "Show Project View" is checked in the first place. If it was already checked, move your mouse below the directories window and see if you get an up-down move arrow. If so grab it and pull it up to extend the project window vertically to a more viewable state.
If it was not checked, the project view may appear detatched from the main window when you check the "Show Project View" checkbox. If that happens, use the "Maximize" button on the detatched window to reattach it to the main window, and then the tiny little "arrow" button where the minimize button for that window section would normally be, to "dock" it among the other windows, so you can see them as well. Each visible window section has its individual controls, so you can arrange them as you like. with respect to the other windows.
It's more confusing to explain than it is. If you look carefully at an open K3b window while reading this, it should make sense
Hope it helps.