I've filled in that I'm self-employed etc, but it's not allowing me to input my T4A commissions amount (the box is locked.) All of the T4 boxes are open though.

You will need to enter your T4A slip first. Then navigate to the Self-Employment summary and choose to edit the T2125 page that the T4A amount has transferred to.

If you have already started a T2125 form, "delete" that one.