2 possible scenarios:
Rent from Japan : If you are already in Osaka then simply come by to look at the apartments. Pick the apartment that you are interested in and you can contract for it. I will require a 1month deposit, and with this deposit you can reserve the apartment 1 month before moving in.
Rent from abroad : You are not in Japan and you want to reserve the apartment online. If you find the apartment that you are interested in online you can simply reserve it one month before moving in. You will need to send a 25000yen holding deposit for this by Paypal. (or if you are already living in Japan this holding deposit can be send by Japanese bank or Postal office transfer) This holding deposit will then be applied towards the one month security deposit once you move in and contract for the apartment.
(If you decide to not move in nor contract for the apartment this 25000yen holding deposit will not be refunded)
You can move into the apartment directly upon arriving in Japan. All the utilities (gas/electricity/water/insurance) will be hooked up in your name.