Thanks, i use win7 64bit, the program i use for serial communication is a c++ (c) i program in vs2013.
Of course when i program the Due(s) or the Uno(s) with Atmel Studio 7, my program is closed so to let the COM ports free and accesible from the IDE.
The problem is (i haven't investigated a lot), some people say the new serial monitor is able to do it, so i have to check.
Otherwise,
i. Both serial Ports don't work together in my case, if the Programming serial resets, i can access the native port but it does not work anymore for serial.
ii. If i disable the programming port and establish communication only with the native then i have to disconnect and reconnect the cable so to make windows identify it, but after this it works ok.