Can I use paper lines if I don't have silicone molds?

Yes, you can use paper liners if you don't have silicone molds. I'd recommend lightly spraying the sides of the muffin liners with cooking spray to ensure that the chocolate doesn't stick.

Can I used the double boiler method to melt chocolate instead of microwave?

You can also use a double boiler method to melt your chocolate if you prefer. Just place a heat-safe bowl over a saucepan and add chocolate chips. Turn heat on medium-low and stir chocolate until completely melted. This is a great way to try if you're worried about burning the chocolate.

How do I store these pumpkin peanut butter cups?

Keep these homemade reese's stored in the freezer. Take the homemade peanut butter cups out and let them defrost at room temperature for 10 minutes before enjoying!