<p>I'm in the process of building the <a href="http://www.thingiverse.com/thing:1001065" rel="nofollow noreferrer">D-Bot core XY</a> printer, and I was hoping to know if the Z-axis 'zero' is near the hot end or near the bottom of the printer furthest away from the hotend? In this printer the Z-platform moves up and down and the nozzle stays at the same height.</p>

Yes, Z-Zero is typically at the "top" of the printer, closest to the nozzle(s). X and Y zeros are also typically in the lower-left corner of the buildplate.
However, the XY zeros are re-interpreted in slicing software to produce cleaner G-Code as it's sometimes difficult to read G-Code in negative coordinates. For this functionality, slicing engines utilize the machine build space length and width.
So if you encounter a situation where your machine "over travels" in either -X or -Y direction during startup, verify that the length and width of your build space is correct in your slicing engine.