I just connected a second ZWO EAF to the ASIAIR Pro (pre-public Beta 1.5) and both EAFs appear in the Focuser Setting window's menu.
However, both devices are named "EAF" in the Focuser menu. There is nothing I have found in ASIAIR that can be used to rename them. Perhaps they can be renamed with some Windows program (ASISTUDIO perhaps?); I have never tried.
You can test with ASIAIR v1.4.4; the current firmware might also work with two (or many) ZWO EAFs.
I managed to identify my two EAF by their "current" positions. One of my EAFs happens to be centered nominally at 50000 and the other is centered nominally at 10000. If you use the same trick for your guidescope and main OTA, perhaps you can distinguish your two EAFs this way too.
And yes, the Focuser control buttons do control the currently selected EAF.
However, I suspect that the (autofocus) button (in v1.5, it is one of the buttons in the array of focuser buttons) will be completely confused unless you also select your Guide scope's camera temporarily as the Main camera (or remember not to touch the button when you have selected the guide scope's EAF.
Chen