If you do not pay the money, then Shopko can sue you. They will likely send you at least one, maybe more demand letters. Then, if you do not pay, if they are serious about collecting, then they will have to hire a (or pay an in-house) lawyer to sue you. They will have to pay a filing fee to file the lawsuit. There is a small chance of them spending good money to chase bad, but it is possible. If you want to try to avoid this, you could write them a letter and send them a check for a significant amount less (say $25), and tell them this is in full and final settlement of their demand. They may or may not accept this.
Since you are charged with a criminal offense, you need to hire a lawyer. You should discuss this with your criminal lawyer and follow that lawyer's advice.
First, I would not send any check until the shoplifting offense is settled, otherwise you would be admitting guilt to the underlying offense, which you may otherwise have a defense for.
If the citation is only municipal, you would not face criminal charges, you will need to see where the return location of your ticket is (i.e. County Courthouse, most likely it is a criminal offense). Either way you would need an attorney. But given that you say it is an ordinance, I will accept it at face value that it is.
I would also doubt that shopko is going to sue you, even in small claims, for $490.00. I checked through computer court records, and they have not been a named plaintiff in Wisconsin in the last few years (they were involved in many as a garnishee, meaning someone who worked there was sued for something, and their paycheck was taken for payment-- so their involvement was a coincidence). Mostly because in Wisconsin, small claims matters do not allow you to recover actual attorney fees. Most likely, nothing will happen. However, if you want to insure you are safe send them a letter offering to settle the matter in total for $25 dollars and write in the memo section of your check "paid in full." Any limiting language on the check should serve to act as a civil defense, and the letter will stop them from using your offer to pay as an admission, as the evidence rules prevent offers of settlement to be used to infer guilt.