Likewise, don't use Metatron boxes unless you have to. You can't store them, so once they're gone, they're gone. In area change mode, always check your map. Remember, your right analog stick is used for fine aiming. Comes in handy when attacking porters or using the sniper gun.
Levels are usually consistent.
That means that the number of squads and items don't usually change. So if you need a metatron or more ammo, then head into the area you got them from in the first place. The more frames you destroy, the more experience. While you do not have to destroy all frames in any area, you usually want to do so to gain experience. Always dash attack.