If you look at the warp core placement on Probert's schematic, the Deflector array clearly doesn't have the same sort of roots that it has on TNG and later vessels, otherwise it would intersect the warp core. As for matter/antimatter storage, above/below the cargo bays looks good.
If you look at the MSD for the Galaxy, they take up a large amount of room. Personally I'd put antimatter at the bottom, connected to the bottom of the warp core, and matter above the cargo bays, connected to the top of the warp core and the impulse reactors.