Assuming you are using the Ampro 100MHz 486 CoreModule, the best place to put the hard drive is on the bottom of the case, assuming you have 3 boards or less in the stack. If you have four boards, which is the maximum you can fit in the case, then put the hard drive on its side to the left of the board stack, but then you will not be able to get the case closed all the way, and this puts the hard drive in possible jeopardy if extreme forces are applied to the case. It is far better to have a 3 board stack and get the case properly closed (I've even sat on top of my case with my full body weight, and not had trouble in this regard). It is important to have the hard drive inside the case. Otherwise it can easily be damaged (e.g. if the rig is in a lumbar pack and you sit down on it, or in a backpack and you lean back on it, the hard drive can be damaged if it is outside the case).
Cover the circuit board side of the hard drive with more cloth tape (thick gaffer's tape works best). Assuming you are placing the hard drive on the bottom of the case, put it upside-down in the case, and use a piece of insulated stiff (single-stranded) wire to ``wiretie'' it down. (See Fig 7.)
Figure 7: Next, the bottom of the hard drive is covered with cloth tape prior to mounting it upside-down in the enclosure. It is preferable to ``wiretie'' it to the bottom to keep it from moving around. Alternatively, you may wish to use angle brackets and the appropriate mounting hardware. Placement is such that it fits under all the boards in the stack.
With the hard drive underneath, you can make a straight run to the header on the CoreModule. Therefore, you can shorten the ribbon cable appreciably (shorter cables all-around make the insides of the rig much neater, and result in greater reliability and improved air circulation). I left the second hard drive connector accessible. The second connector may also be left protruding outside the case if desired. This makes it quick and easy to do backups or copies (e.g. to help someone else get a system up and running) onto a second hard drive.