Stephanie, Honesty is probably the best way. Since she knows you had sex already, it should not come as a surprise to her. You can add that it will help you with your irregular cycles and PMS.
You will however also have to protect yourself from STDs and infections. Having sex without condoms is a real no-no at your age. With every guy that ejaculates inside you your risk for bacterial infections increase.
There are many polyurethane condoms for couples with latex allergies. These are very thin and putting a drop or two of personal lubricant in the tip will make the experience much nicer for both of you.
The only safe option for you at this age (except for abstaining) is to use both condoms and the pill.
If you were my daughter, I would encourage you to rather use other forms of sexual play and avoid intercourse. Depending on the state you are in and your boyfriend's age, he might also be committing statutory rape, even if you consent.
Take care!