Travel as light as possible. There will be lots of walking and transferring between different rail or metro operators to get into the city, then near where you are staying in Tokyo. The lighter you pack, the easier this will be.
Spend a few nights and move to another part of the city. We stayed near Tokyo Disneyland which was great for that visit, but was really long getting to sights in the central business areas of Shibuya or near the imperial palace. The travel times were just to long to see everything we wanted in other parts of the city. Tokyo is really a collection of different cities, so the travel times can be quite long, especially with connections on various metros or train lines.
There are a number of different train operators in Tokyo which can get a little confusing. I noticed they now offer multi-tickets for Metro to JR rail for instance, which would normally need two separate tickets. Keep this in mind if going to buy day passes on JR Rail, Metro or the Kesei Line servicing Uneo station and Narita Airport; these are all different companies. Here is more information on transportation around Tokyo, which is run by 11 different operators!
Vending machines are ubiquitous around Japan. You will see them on the streets in cities and residential areas. Mostly they are cold drinks, but can be for food, hot drinks, toys or just about anything else! You will quickly realize how convenient these are when walking through the city or park deciding it's time for something to drink. No need to carry a drinking bottle around with you in any Japanese city, you will be surrounded by these!