Just to add to the Pocket Concierge experience, as explained upthread, everything is prepaid so depending on timing of your visit and when you made the reservation, you might get the credit before your visit which was my case. Booked two weeks in advance and credit received before I went to the restaurant.
Payment for any extras not part of the course (like drinks) will generally be automatically charged by Pocket Concierge so at the end of your meal, you just tell the restaurant you're done and walk out. I found out one place charged 770 yen for mineral water and 880 yen for sparkling water only afterwards when I saw the Pocket Concierge charges. Had I known we would probably have ordered more drinks for the same price but that's a restaurant issue anyways and nothing to do with Pocket Concierge. I believe some restaurants would ask you to pay the extras on the day though.
Also make sure that you are not paying for the reservation again at the restaurant. One time the waitress asked me to pay (didn't order any extras) so I told her I paid online already which she confirmed so sometimes they might miss that.