The Antimatter would have to be enclosed in a magnetic bottle, with a vacuum around it, to keep regular matter away, until it was ready for detonation, of course.
Nah...
When I was a kid (1960s) I designed an anti-matter spacecraft that simply stacked two particle accelerators (the round kind) on top of each other: one produced a certain stream of particles and the other produced the appropriate anti-matter stream of particles. The two accelerators would simultaneously throw their carefully calibrated streams of matter and anti-matter into a chamber where the resulting collisions would produce the violent explosions necessary to become a propellant force.
In other words, there is never any need to store anti-matter - - it is created and used as needed.
I must have doodled 200 versions of this craft.