If you'd like useful suggestions, the first thing you need to do is post your recipe.
Peanut butter cups are made by piping peanut gianduja into tempered chocolate shells, allowing the gianduja to set up, then capping with a thin layer of more tempered chocolate.
Make the gianduja by grinding 1 part roasted peanuts with 1 part sugar in a food processor until smooth, then fold in 1 part melted chocolate. The resulting gianduja will have a smoother texture and set up more quickly if you warm it to about 40C then work it a few moments on the counter with a spatula before you fill the shells.
Tempering chocolate is a topic for a different post.
There are plenty of quick & dirty shortcut methods, but the above is how artisan chocolatiers (e.g., me and my staff) teach and do it.