EMCON, or Emission Control, is a Doctrine you can set in Command. Using EMCON, You can specify whether or not active sensors should be used, whether at the Side level, Mission level, or unit level. This is significant, because active sensors can be detected by means of SIGINT aircraft, at tactically significant ranges. Using passive sensors degrades quality of information as well as range, but can prevent your units being detected by hostile forces, or at least prevent their being ID'ed by the enemy.
The highest level setting for EMCON is at the Side level. Setting EMCON at side level will provide the default EMCON settings for the entire side - any unassigned units will by default follow EMCON, unless told otherwise. This can be done by clicking the 'Game' button in the menu, and selecting 'Side Doctrine and ROE' from the list. In the subsequent window, select the 'EMCON Settings' tab.
You can override this at the Mission level. In the Mission Editor window (Missions + Ref. Points->Mission Editor), click the Mission Doctrine/ROE/EMCON button, and the same window will be displayed. However, in this context the settings will apply only to units assigned to that mission (assuming "Enforce EMCON Obedience" is set). In this case, you could set Side doctrine to have only passive sensors, but units assigned to your mission could have OECM active.
This can be further overridden at the unit level. When you select a unit, click the Sensors button. This will display the same window again, however in this context it only applies to the selected unit. In this manner, you can set a single unit to have its sensors go active or silent.