Alright, thank you for the input, but this does not work with the phantom. After experimenting a little with friends, I found only the co pilot is able to lock guided weapons such at ATGMs, AAMs, and GBUs, which is problematic considering the pilot has control of the missiles by default. Through editing the pylons in the editor/zeus enhanced, you can give the co pilot these weapons, and the co-pilot CAN use the radar and gunner cam to lock things, meaning pressing R and T will work as it does in normal arma jets if you're in the secondary seat.
It's better to give the pilot dumbfire munitions such as unguided bombs, rocket pods, etc. And to give the co pilot your AA missiles, GBUs and ATGMs.