The Amazon River is the largest and longer river in the world; it's also the main artery of the whole Amazon rainforest system and washes most of the villages and towns in the region. If you make a trip up or down the Amazon River you will have the opportunity to know the ecosystem in all its plenitude .
The first thing to decide about a trip in the Amazon River is if you are going upstream or downstream. Both ways you have regular boats linking Belem and Manaus in a 5-6 days trip where you stop at the most important cities in the Amazon rainforest region, like Santarem and Parintins. There are always boat cruises especially designed for tourists. They are more expensive but you have a trip fully designed to foreigners and all the things you need, so you just can relax.
Let's see in detail one of those trips, starting in Belem and going to Santarem . Belem is a big city and you won't have any problems there. The trip started in Belem river port where you can easily get information (including information in English) about the boats that are leaving that day or the next. Choose the boat you want to go (they will vary on speed, accommodations and price) and pack yourself, don't forget to buy a net if you are not going in a cabin (think carefully about that, comfort in a cabin pays off the difference in price by far). The travel usually starts early in the morning and you will see the first nice scenes within just a couple of minutes from the start of the trip. Actually, you will get astonished after a couple of hours when you leave the traces of the big city behind and start to see the forest.
Along the way the boat will stop in numerous villages on the river banks, these villages vary from size but all of them are very poor and this can be quite shocking to some people. Although it's already expected, extreme poverty is always something hard to see live. But don't worry, after a couple of villages you will start to feel that besides poverty the people are quite happy and friendly The village children are very curious about foreigners. Make contact with them, buy some goods (fruits, collars, feathers.), interact with them and don't forget to take pictures. You can go off board on these villages and take small walks through the forest, be sure to know how long the boat will stay on the port, as that varies from minutes to hours.
Make friends in the boat, you will spent a lot of the time on the deck taking pictures and talking. If you are the only foreigner on the boat you will have to master your mimic skills and talk with the locals (it's not likely that no one in the boat speaks English but you should be prepared for that). Since the local population is friendly and warm you will have a lot of friends at the end of the trip, and you will be surprised how much we can communicate without sharing a common language. At the night a good thing to do is stare at the sky full of stars (without any big city around the sky is very clear and you can see many more stars than in any city of the world).
A good way to do this trip is go just half-way up the Amazon River until Santarem, a small city but one that has an airport with flights to Manaus, Belem and Rio. Take a few days in Santarem and in the local port hire smaller boats for a day ride or just some hours. In those days you should enter the smaller river branches and flooded areas to get real close to the forest. There is also trekking trails you can do. After your small stop you can decide if you want to get a plane to Manaus to continue your trip from there or to take another boat upriver. From Santarem you can continue until Manaus doing small trips from one city to another, you can stay in Parintins and Itacoatiara before you arrive in Manaus .
In Manaus you should make small expeditions in the Rio Negro , this river has an water composition that prevents mosquitoes and that's very nice! You can sleep in the open and not be concerned or bored by them.
Another option may be to start in Ecuador where the tributaries of the Amazon river like the Napo River begin. This will give a different perspective than starting your journey where the river is wide and fast flowing. There is not a single way or tour to make in the Amazon rainforest, your trip will depend on how much time you want to spend and the trade-off between comfort and going into the most remote areas. Either way it will be an unforgivable trip.