To create an antimatter missile, you need three components: the antimatter head, a mechanism for the head to explode at the proper time, the missile itself.
1. Antimatter head
While matter is made of electrons and protons, antimatter is made of the opposite: positrons and antiprotons.
Using common physics class knowledge, electron is a small particle with a negative charge and very little mass. The proton is also positively charged with more mass than an electron. Since an electron and a proton has the same charge, just opposite so that they can cancel out when added up, I'd tell the electrons and protons of all the atoms in of a certain object to conserve their mass while reversing their charges.
I doubt that MC is able to remember the elementary particles that subatomic particles are made of so That's as far as I'll go. However, if MC does remember those, then MC can just tear atoms apart into their elementary particles and reassemble them to form antimatter.
Since this all depends magic and imagination, he could even go into String Theory if he understood whatever that is.
This probably takes a ton of mana soC probably need to set up an automatic mechanism to auto-create antimatter and store them with magic to keep them separated from matter.
As for which element, it has to be stored easily so I think anti-lithium would do. It's a metal so it'll be stored easily.
2. The mechanism to activate the antimatter.
I saw a YouTube video in nukes and they apparently triggers midair for maximum destruction because the air waves from the initial explosion would combine with the air wave reflected from the ground to form a very powerful and wave that travels outwards from the explosion on the ground. So the antimatter probably must be triggered midair. 
Using logic gates coded using magic, the missile can know when to trigger based on it's distance to the ground. The trigger mechanism probably has to be the missile itself since it is the densest source of matter nearest to the antimatter head.
It will trigger by deactivating the antimatter-matter barrier. The accelerating missile is force enough to ensure that the antimatter and matter collide.
3. The missile
Using 8th grade math, that ax2 + bx + c thingy, The trajectory of the missile can be graphed.
Might as well build a calculator with magic.
The launch is just a directed explosion which uses oxygen and hydrogen from the surrounding air as fuel.
In case the opponent has magic barriers, maybe some automated anti-magic things to break those down.
And done, you have an antimatter missile.