As far as I recall, ChemDraw is an illustration program. To run a calculation in ATK, you need the actual coordinates of the atoms, e.g. in an XYZ file. Perhaps ChemDraw has such an export function, and in that case you could do it. I would doubt that it does, but on the other hand it does have "interfaces" to QM software like MOPAC, so perhaps...
Otherwise I suggest you use a real molecular editor, like those in VNL or some external software that can produce an XYZ file.