I needed to run Pencil through a desktop launcher, because I don't wanted move on to the Pencil's directory and run npm start everytime I wanted to use it.
Then I've created a simple script to solve that in a file called pencil, and I put it into /usr/local/bin.
It basically uses npm start --prefix to pointing to a place from where it must be run, and nohup to run it in background leaving the terminal free.
You can redirect output message to /dev/null 2>&1 & if you want as well.
Don't forget to replace /path-to/pencil of pencil file by your system path to Pencil, and give it executable permission.