Hi Ricky,
Just set up a FENE potential between the given pair of particles, and an LJ potential between the given particle types (probably the same type) and you get exactly what you want. This is the standard setup which is just described in a weird way in the paper that you cited.
The fene potential acts just between the two particles with a given id. The LJ potential acts between any pair of particles. If your pair of particles interacts both with fene and LJ, then you get the fene+LJ interaction.
See also the script minimal-polymer.py in the samples directory.
peter