Chris,
Please refer to the TREQ-L User Guide, section 5.3.1 (page 40), which discusses the keypad driver and how to use the DeviceIoControl interface to remap keypad keys. Code examples are also provided in this section.
http://www.qsicorp.com/pdf/qsi_treq-l_user_manual.pdfRemapping keys through this interface (e.g. via the IOCTL_KEYPAD_SET_KEY control) will cause a change to the current key mapping and a corresponding setting in the device registry (also described in section 5.3.1). The registry is persistent, thus your key mappings are persistent, even after power has been removed and reapplied.
The EMG key (TREQ_KEY0) can be remapped from its default function (VK_RUN_APP) to another keycode, such as VK_F1 using the DeviceIoControl interface with the IOCTL_KEYPAD_SET_KEY control code. In your message pump for your application, you would then intercept WM_KEYDOWN messages and filter based on the keycode that was pressed.
QSI provides a set of C# wrappers for the C++ DeviceIoControl calls. These are available for download from the following link:
http://www.qsicorp.com/engfiles/TREQ/Apps/TREQDriversNetCE_DLL.zipDocumentation for these wrappers is included in the zip file.