EC25 custom SW interface

Dear Forum.
We have a simple Software interface on Window and Linux PC, that connect to a old module via serial port (the module use UART, the a UART to USB bridge show us a COM on window); so, via AT command, we send SMS, receive SMS ,connect to GPRS ecc…Enough simple .
Now, we wand to move to the EC25 or EG25,but not using only UART, but using USB also for data speed .
This start my confusion : I install a Window driver ,and connect my EC25 to the USB of PC.
Question are:

  1. Where on window (same will be for linux )I can see my AT interface ,and where my USB for send data?
  2. If i use AT command, why I see example with PPP or QMI or ECM …Why I need this protocol if AT commands can -command- the module to SMS, TCP IP ecc…

Thanks very much,and excuse for long mail.