Aten has been published in the Journal of Computational Chemistry, and the article can be found online here. The full reference is:

"Aten - An application for the creation, editing, and visualization of coordinates for glasses, liquids, crystals, and molecules", T. G. A. Youngs, J. Comp. Chem., 31, 639-648, (2009).

It is not a requirement to cite Aten in your work, but if you feel that a citation is deserved because it has been particularly helpful, then please feel free!