To the OP, we had our bags shipped via Yamato (ubiquitous black cat logo) from Century Southern Tower to arrive at our hotel in Kyoto a few days later. The little convenience store behind the lobby desk and near the hotel elevators is where Yamato does business. We got the ticket there and had the front desk help with writing it up for us.

Since we were leaving the CST before the convenience store was open we dropped the bags off at the store the night before.

We didn't need the bags for a few days since we stopped on the way to Kyoto in Hiroshima and Miyajima and stayed one night in each city. All went smoothly and our bags were waiting for us in Kyoto.

You can even select a time range for your bags to be delivered if it is important. We did this Kyoto to Tokyo since our Tokyo hotel would not accept the bags until after we had checked in. That also worked out perfectly.

With no concierge at CST I suggest not waiting to the last moment and you talk to the lady in the convenience store to find out what you need to do and by when. FYI, she didn't speak much English and some of the desk clerks didn't either. Our ticket was filled out several days before we actually left the bags at the store.

BTW, we loved our 5 night stay at CST...corner room with fabulous views of Tokyo.