We are going to use COTS Atom mother board, there are two types of motherboards: Commercial(cheaper) and Industrial(expensive).
With commercial boards there is no documentation, how can I ensure if the Watchdog is already supported on these boards.
COTS IA32- systems that have ACPI support will have ACPI tables exposing the watchdog resources. You can probably look at the acpi tables and/or BIOS documentation.
ACPI spec has facilities to expose watchdog timer resources to the OS.
If the board is not designed to run windows (lack of acpi support, custom linux kernel support only), then you have to look at the hardware specs, i guess