Melt 3 cups chocolate chips over a double-boiler. For best results place the muffin tins into two cupcake tins to equal 24.
When the chips are melted, place 1-2 Tbs in each liner. Gently rub around until the bottom of the liner is covered. You want at least a 1/4 thickness. Allow these to cool and harden.
Mix up the peanut butter mixture. Start with 1 Tbs of nutritonal yeast and taste before adding more. The Adams that I used has no sweetner and very little salt so I added salt and powdered sugar until it was sweet enough. I just sifted the sugar into the bowl. If the peanut butter is very firm, microwave it or place it over the boiler for a short time. However, you want to put it in the fridge and firm it up a bit again. I did not do this and had some trouble later.
When the chocolate is firm, place one Tbs of peanut butter mixture in the center of the cup. Don't spread it around some will spread as you add the next layer of chocolate. I made the mistake of leaving the PB soft and smearing it around. When I poured the next layer of chocolate, it did not meet the first layer and seal the PB inside. When I did some more I tried not to spread it around but it was too soft and still ended up going to the edge. Next time I will firm the PB mixture up in the fridge before proceeding.
Melt the rest of the chocolate to cover. You may not need the whole 3 cups. I was able to make 6 additional pb cups (30 total) with the amounts listed here and I only used 5.5 cups chocolate total. Spoon the chocolate over the PB and gently smear around. Also you can tap the trays to get the chocolate to settle down and work out any air bubbles.
Place the finished cups into the fridge and chill completely before removing the papers.