My granddaughter has an epi-pen. Instructions on when to use it were included in the box. If you didn't get them, I urge you to talk with the prescriber or the pharmacist about when to use it.
It's for life threatening reactions only, when breathing is compromised.
I also have food allergies and often had bad itching on my tongue and lips. That is definitely not cause to use the epi-pen. Neither are bad hives in and of themselves. I don't know what you mean by body swelling. did you take him to the ER after administering the pen? If he didn't need further treatment, I suggest that the pen might have been overkill.
Allergic reactions are scary. Over time, with experience you will get a sense for what is going on. The epi-pen is for infrequent emergency relief and definitely should not be administered in lieu of prevention. Be sure to keep the foods to which he's allergic away from him. Every time he has an allergic reaction his body is building up more anti-bodies that may eventually make his reactions even worse.
I've had couple of anaphylaxis episodes, caused by a bee sting and a medication, which in today's world would've required an epi-pen. At that time, the doctor administered an antihistamine (Benedryl) and probably something like what's in the epi-pen.
I suggest that for the allergic reactions that you've described giving him Benedryl would've been the appropriate treatment. My granddaughter has had the intense itching and hives and a full dose of Benedryl relieved the itching and the hives were gone in 30 minutes.
Do talk with her doctor or a pharmacist about the epi-pens use. Ask for a description of specific symptoms that would benefit from an epi-pen. I suggest that the inappropriate use can result in difficulties. It contains an ingredient that gives a powerful boost to his body. I'm not sure but I think it increases heart rate as well as reducing swelling. I suggest using it when it's not needed puts the body in undue stress.