You have some control over the stdio window with functions in the utility library:
SetStdioWindowOptions()
SetStdioWindowPosition()
SetStdioWindowSize()
SetStdioWindowVisibility()
It sounds like your user interface includes both the stdio window and the UIR user interface. Normally I use one or the other. I use the stdio window only for the simplest applications where I'm just looking for something temporary, quick and easy. I use the UIR (without the stdio window) for just about anything that I'll distribute. I would suggest not using the stdio window at all. You can use text boxes to get user input from the keyboard or to display messages to the user.