Well it's kinda confusing. Easy place for an "off by one" error.
What they mean is that you control the third variable in the table- on the VE table, for example, you have kPa and RPM as two "dimensions", and you enter the third "dimension" (the VE value). If you hit the graph button, you'll see a 3-D representation of your "3D" table. On that graph, you have RPM and kPa as your length and width, and the VE value as your height, hence a 3-D table.
A 2-D table would be something like the idle speed vs. CTS - this only has two dimensions (and in this case, you program the graph instead of values).
I don't know if that makes sense, but I did my best.