I have now installed Puppy Linux, I am having trouble getting it to mount the CF reader
You can go to start>utilities>mount/umount... and see if it is listed. It will probably be sda1 but it could be something else depending on what your using with usb.
Then go to where it's mounted with Rox or rxvt to take a look inside, but you will need to umount it for fdisk and reformatting.
If you still have problems you should check on Puppys Forum. Barry has just added the latest 'Puppy drive mounter' program to the system and all of this info is on the Puppy Linux Forum.
Greg