Mechs locations are color coded as to weapon type. For example only ballistic weapons may be placed in a ballistic weapons bay. Clan mechs have a certain number of omni bays in addition to their regular bays. As an example, the Daishi, a 100-ton Clan mech, has one missile bay in the head, two ballistic bays on the right and left torso, two beam bays on the right and left arm and three omni bays, one on each arm and one in the center torso. These bays come in different sizes, as do the weapons.
Weapons take up from one to three slots.
Big bays are usually located in the torso, with smaller bays on the arms and head. Omni bays in the Daishi's arms have two slots, as do its two beam bays in those locations, while its center torso omni bay has four slots. So, if you want to put a PPC on a Daishi, it can only go in the omni bay in the center torso and nowhere else. More importantly, it means that mech choice won't just be about how big a beast we can mount, it will have to do with what weapons we prefer and how they fit into a particular mech. There's going to be a of juggling going on in Mechlabs everywhere.