I might not be the best person to reply to this question, but I think I can answer it anyway.
Unless the pair_style you plan to use explicitly takes custom atom properties into account (and I'm not aware of any that do this), you will have to create your own pair style that does. If this is not possible for whatever reason, you can accomplish the same thing by writing your own fix that loops over all pairs of nearby atoms and applies a force to these atom pairs. (...as opposed to creating a new pair_style. See fix_bond_create.cpp for an example how to loop over nearby atoms.)
Don't know if I helped.