Just use one GUI and put all controls on that. It's annoying for the user to have multiple windows that can get overlapped, hidden, misaligned, etc., plus you have the difficulty as a programmer when you need to make variables in one gui seen in the other, separate gui. Why not just avoid all that and have a single GUI?
That said, if you want to ignore my advice, it can be done. See the FAQ: http://matlab.wikia.com/wiki/FAQ#How_can_I_share_data_between_callback_functions_in_my_GUI.28s.29.3F, which actually also holds for single-GUI apps where different functions need to share variables.