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 SourceCode examples.
For testing you can also read/write registers with our Colibri Tweak tool.