It is also possible that they differentiate by color. Since the new TOS phasers are red, maybe the torpedoes will be blue? (swapping the colors would completely screw with the canon, since quantums are blue, but who knows)
Actually, Federation photon torpedoes were usually blueish-white during TOS, and even in TMP. No canon violation there at all.
Also, phasers during TOS varried between blue and red on a regular basis. Hand phasers were even green on occasion.