In order to get Windows Embedded CE to run on a specific hardware you need to have what is called a Board Support Package (BSPs)." This one contains drivers and low layers for the OS specific to a board.
Whether you develop your own BSP or get one from a SV or IHV, you install it on top of your Windows Embedded CE 6 toolkit which allows you to build, deploy and debug OS images for your hardware.
You can find the list of available BSPs for Windows Embedded CE 6 on this page. Note that there are 160 of them!