This is an interesting post....
Some relevant issues:
1) Unless you agreed to be a 'responsible party' when taking a customers check, you have NO liability to the store owner to make the check 'good'. Ask the store owner to show you either your agreement, or your acceptance of the store 'policy'.
2) Unless the store owner gets a court ordered judgment against you, they CANNOT 'garnish' your wages. Any withholding of your pay without your permission would be illegal and probably a violation of local and federal labor laws.
You now have a decision to make.... and either choice is going to result in your probably losing this job.
a) Confront the owner and challenge the 'involuntary withholding'.
b) If he decides to 'withhold' anyway, you will need to report him/her to the local labor folks and probably have to sue him to recover your pay.
In any case, start now by documenting the 'case'. Get copies of all paystubs, notes, memos, etc.