I started playing the commanders edition and realized I can't manually launch surface to air missiles because it's all automatic.

That saddens me. Is there anyway I could change that so I can launch them myself? Thanks! (sorry if I did anything wrong. New to the forum.

)
Unfortunately, there is no manual control option for air defense in HCE at this time. For now, you're restricted to modifying your (1) rate of fire and the (2) engagement range, as follows:
For rate of fire, go to Settings/Staff Options/Surface SAM Fire Rate in the task bar. As a rule of thumb, the 'Light' option means 1 SAM vs 1 target. 'Normal' means 2 SAMs vs 1 target. 'Heavy' means 3 SAMs vs target.
For engagement range, go to 'AAW Auto Fire Range' under the same pop up window.
Shutting down your radars will prevent launch of radar guided SAMs, but that might not be a good idea in the face of an attack.