Hi, Tony:
The main reason why Canon advises users not to stack extension tubes or other coupled lens accessories like extenders is the possibility that the camera's shutter may not release. Each extra accessory increases the level of electrical resistance. But, you are welcome to try; many users have reported successful results using 2 or 3 coupled extension tubes.
Autofocus performance with extension tubes is a separate issue. Assuming no problems with shutter release, there is still the possibility that the effective maximum aperture of your coupled lens with one or more extension tubes may become smaller than f/5.6. If so, the camera's AF system may not be getting enough information to determine an accurate focus. Additionally, extreme close-up photography results in extremely shallow depth-of-field. Even if the subject matter is reasonably contrasty and the effective maximum aperture isn't an issue, the focusing motor in the lens might be driven so fast that the AF sensors can't recognize the subject. This is not to say that AF with extension tubes is impossible, but it's important to realize that the odds are stacked against it.
Manual focus is often the only practical option, even when autofocus is technically available. Under such circumstances, you may find that focusing manually while pressing the shutter button halfway allows the circular green LED in-focus indicator in the camera's viewfinder data display to function as an effective focusing aid.
Hope this helps!
Best Regards,
Chuck Westfall
Director/Media & Customer Relationship
Camera Marketing Group/Canon U.S.A., Inc.