本指名 = Nomination whereas 指名 is just a name that you designate. They essentially are the same thing in the overall picture.
Most places will charge you a nomination or name fee if you choose the girl yourself. Otherwise, you just get a 'free' assignment on whomever the shop picks for you. (which can really be a disaster in some cases...)
That makes sense, I'll definitely keep an eye on whether I get double charged in the future.本指名 is supposed to be when you have 指名'd the girl before and now you want to do it again.
Some places will definitely put charges in top of charges as long as they get away with it.
Thank you both for the replies!