In a restaurant, the correct thing to do with your napkin when you go to the ladies' room is to place it on your chair. This action signals to the staff that you intend to return to your seat and haven't finished with your meal yet. Leaving the napkin on the table might give the impression that you are done with your meal, and the staff may begin clearing the table, which could be inconvenient when you return.
When you leave the table temporarily for any reason, whether it's to use the restroom or for another brief absence, placing the napkin neatly on your chair is a common and polite practice. Upon your return, you can simply pick up the napkin and continue using it throughout the meal. At the end of the meal, you can leave the napkin on the table to indicate you are finished, and the staff will take it as a signal to clear the table.