You can access HW registers directly in your SW. This is possible in Win CE 5.0 / Win CE 6.0 / Windows Compact 7. Make sure that you use our MapRegLib.lib to be compatible with Win CE 5.0 and Win CE 6.0.
You can find a sample in our free [Article not found #100630].
For testing you can also read/write registers with our Colibri Tweak tool.