The best way to describe the difference would be: Old School. Its like a trip to WDW back in the 80's-90's where you could just show up and have a great time without worrying about booking a fast pass in advance. When are you going? I would suggest taking a look at this page:
http://info.tokyodisneyresort.jp/en/schedule/stop/stop_list.html . It describes the current and upcoming annual refurbishments for attractions and other facilities at the resort.
Fast Pass is still the legacy paper based system. Basically, you show up at the attraction of your choice, scan the QR or bar code on your ticket in the machine and you get a paper ticket giving you an hour window to return. Tokyo Disney is very strict when it comes to those times and unless the ride broke during your one hour period, you can't be late. When you can get another fast pass? Either when your fast pass is valid or a two hour window has passed. I will give you an example: say you score a fast pass for Toy Story Mania! for 12:00-13:00 and it is currently 08:15, you can take another fast pass for a different attraction at 10:15 or wait until 12:15 to get another one for Toy Story Mania! if they are still available. Fast Pass are in limited quantities and they can run out fast for the more popular attractions.
Knowing that nearly everyone at the parks use the fast pass system, you have to play along with it and use it to the max. Say that you are in my previous example, at 10:15 I would be standing near Tower of Terror and as soon as 10:15 comes around, I would score a fast pass for TOT. The highest demand attractions at each parks are:
Tokyo Disneyland: Monsters Inc. Ride and Go Seek, Pooh's Hunny Hunt, Splash Mountain.
Tokyo DisneySea: Toy Story Mania!, Tower of Terror, Journey to the Center of the Earth.
Seeing that currently, everyone at Tokyo DisneySea walks quickly to Toy Story Mania at opening and quickly empty those machines, skip that ride. The only unique part is the beautiful facade outside. Instead, go on the right of McDuck's Department Store and head to Tower of Terror. You can score a fast pass quickly for that and then head toward the center of the park. Ride Journey to the Center of the Earth in stand-by as the fast pass line only opens 30 minutes after the park opens and you will quickly get on. Notice that I don't talk about Raging Spirits and Indiana Jones Adventure. They both have very efficient and fast Single Riders lines and use your valuable fast pass opportunities elsewhere.
At Tokyo Disneyland, Monsters Inc. Ride and Go Seek is my first stop for a fast pass and then I quickly walk to Pooh's Hunny Hunt, getting on in stand-by while everyone else is waiting for a fast pass. Depending on how fast you did it and if you use early entry due to being an hotel resident, stay in the area and ride Space Mountain or Buzz if the line is under 30 minutes or its not yet 30 minutes after park opening. Tokyo Disneyland has one single rider line: Splash Mountain. Like at Tokyo DisneySea, walk up to the entrance, hold up your finger in a one pose and ask "Single Ridah?" They will direct you to the right place and if you go into the Fast Pass line, do the same at the merge point.
Priority Seating wise, they take them 30 days in advance, but its online and in Japanese only. I instead waited until the day I visited, got my first fast pass and then at 10 am, went to the restaurant I wanted to eat. You can then make a same day priority seating at the podium if any times are left. Else, you will need to wait in a stand-by queue.
You are staying at Disney hotel and thus, you are allowed a 15 minutes early entry into the parks. Normally, day guests will start arriving 90-120 minutes in advance before park opening and sit down in front of the entry gates. In your case, you can arrive 30-45 minutes and go to the early entry turnstiles. At Tokyo Disneyland, you are allowed to ride Buzz Lightyear during that period and have access to World Bazaar (their Main Street) and part of Tomorrowland. Once the park opens to everyone, you are in prime position to score a very early fast pass for Monsters Inc. or Pooh's Hunny Hunt. At Tokyo DisneySea, its the American Waterfront New York area that is open and you can get on Toy Story Mania and Tower of Terror early. Once the park opens to everyone, you can quickly access Port Discovery for the new Nemo attraction or go to Mysterious Island for Journey to the Center of the Earth.