The 'fullscreen' part is the problem. If you are running under a GUI and you run xterm as fullscreen, you are defeating your own purposes. Fullscreen under a GUI like x-windows is almost redundant, as the 'fullscreen' mode will not let other windows appear. Games like to use fullscreen mode, simply because it allows them to have complete access to video cards resources, and set the video resolution to whatever they want, without concern about what other applications might need.
You can run everything from a command line, but you cannot do it when an xterm (or anything else) is fullscreen, because everything you run will not have access to the video card. A better solution would be to open a xterm like normal (windowed), and run things from there, or instead of running fullscreen, you could simply maximize the xterm window. That would allow the xterm to take the most screen area, but allow your programs to pop up as well.