I am a little confused. When she got out of jail, you gave her back the kids, and now she wants to collect child support from you but they are saying you owe from when you had kids?
File for modification based on you had physical custody for the period of XX to XX. That father agrees that the current amount for child support should be XXX however the arrears needs to be readjusted to reflect the time father was providing for care while mother was in jail.
If this just went to court and you were not there, you could also file for an appeal. A modification will probably be easier...
You can file yourself at the family court house. Type up a little blurb like above with all your court papers/divorce papers. They will then give you papers to have her served and a court date. Here is it free (some states there is a small charge) and you get a date in 3-4 weeks....maybe a little longer with holidays coming up...