For the first case, you can manage to hide your main panel window using gtoolbox window management (gtoolbox.topcool.net) or LVUTIL32 at NI website. This way, you can hide the window to avoid anyone to mess with it.
For the second, you should have both vi's in the same level, i mean that if you put the secondary vi inside the while loop of the primary, this will wait the secondary to finish, so, you'll have to either call it dinamically or outside the main loop.
Hope this helps