If I can boot off the onboard CF device what device does it come up as?
still hde?

yes, ide.

Here is the problem I am running into:
On the stock bios I can not boot off the CF, so I boot off a hard disk.
Well, when I add linuxbios, the system will be asking for data before the
hard disk will be ready. My hard disk has a 5~7 sec spin up time. So in turn
I plan to boot off the CF so solve this problem.  OK, fixed the spin up time
problem, but brought up a new problem.  My current kernel config loads the
ide-cs (access to the CF) after software suspend 2. So software suspend does
not work, as it can't read the software suspend file during boot;  ide-cs is
not loaded yet, and I don't know how to change the device loading order in
the kernel.

ide-cs ? that's part of pcmcia, it shouldn't have anything to do with cf at all if you are are connecting CF via IDE bus (which is the way you should do it, and which should the the way if it is on board cf device).
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