One Big Mess
In all probability, all cartridge firing firearms at the scene will be taken as evidence until the ballistics boys identify which firearms were used or discharged. As an investigator, you don't want to be flayed on the witness stand for assuming that only the gun in the home owner's actual possession was used.
Another point to remember is that once you have defeated the intruders, you are now responsible for them and you may not permit further harm to be inflicted upon them by family members. It is wise to call 911 and advise them that medical assistance is needed. That 911 tape will be entered as evidence so choose your words carefully and do what you can to prevent the wounded intruder from dying if you can safely do so.
Int'l Assoc. of Law Enforcement Firearms Instructors