Quote:

"... It homes to the top - so it thinks that's 0.  I would like z=0  
to be at the top of the material so that z moves will be made in  
relation to the top of my material rather than from the top of the
axis."

As it should.

Micheal there are a few terms which may be a bit confusing at first -
which is why so many DIY types often shortcut proper procedures. But
tsking time to learn it the right way will quickly prove faster, safer
and much more reliable.

There are Zero's and then there are Zero's

Your Machine should home (zero) to its machine coordinate system aka
G53. (This location never changes)

>From there you will define your Work zero (most commonly starting with
G54) (defined from the G53 location and depends on the work)

And finally there is your Tool length offset aka Tool zero which would
be G43 H## ( or G43.1 or...)

The above are just a basic outline and EMC2 is so flexable that this is
not etched in stone.

Understanding G-code is a long process, but the coordinate systems you
will be using is one of the first topics you will need to understand.

Best I can say is read the manuals, if for nothing else of identifing
what questions you need to ask.

Greg

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