Open ZK-lobby -> SETTINGS -> Skirmisher -> Select engine 100.0, Zero-K 1.3.8.14 (or whichever is the latest) -> select map, set options, add AIs, move around boxes, etc as you like
For AIs you should probably use "game's AI"s, others might not work properly. Not sure how or if you can change box sizes, but you can move them around with your mouse.
(note that your background color will probably not be black, I changed mine manually in the SETTINGS)