How does F/A-18 autotrack work?
Autotrack means the FLIR (Forward Looking InfraRed) sensor attempts to track whatever object falls inside the tracking area. It means whatever the pilot was trying to keep up with was producing emissions in the infrared (heat) and the system was automatically tracking it.

Boxing a moving target is having the tracking system detect and track a target you have selected. In this case, the other pilot was asking if he had selected the target manually (boxing) or if the system detected and autotracked the target on its own.