Before discussing anything about the Indians, I'd like to say that the tribes of the same level of development do not differ in attitude. All the claims such as "Tupi are friendly", "avoid Arawaks", etc. are baseless.
The Indians' attitude depends on game level and your behavior - how far from them are you keeping your colonists and military, how often do you trade with them, attack them, or steal their land (before Minuit), how many missions have you established, do you have Pocahontas, are you playing the French? These are the basis of your relationships with the Indians, not identity of their tribe.
As tribes of different levels have varying characteristics, it's fair to assume it has some effect on their attitude, but mainly through secondary factors - you're more likely to have considerable trade with more civilized Indians, take lands from agrarian tribes, etc. The difference is however rather minor.
Prepare for a big war against the Indians. If they're close to your colonies, they will attack, either because they just don't like you, or because the king pays them to. (Unless you play the French, get Pocahontas early, establish many missions, trade with Indians a lot and hope for some luck, in which case you *may* avoid it, but you probably won't want to avoid it).
Many benefits come from attacking Indians.
First, you get treasure. They're really worthwhile in case of the high-tech Indians (Aztec, Inca), but a bit of free money from the low-techs won't hurt either. Cortes greatly increases the amount of treasure you can get, so get him before you start a campaign (unless you have to do it earlier to protect your colonies).
Second, if you have a mission in the village you're attacking, there's a big chance that they will join you as converts. Converts are quite useless in the mid to late game, as you should have a lot of outdoor specialists, but you can convert them all to free colonists with Casas. Chances for conversion are pretty small without Sepulveda (I think you're more likely to lose a missionary than gain a convert), so get him or don't establish missions during the assault. I don't know how the missionary's expert status (Jesuit or Brebeuf) affects that chance.
Third, attacking Indians is the easiest way of training your soldiers before the war with the king. After you have George Washington, every successful attack results in the soldier being promoted to veteran status. And occasional failed attacks result only in the loss of 50 horses (50 horses for upgrading 3 Free Colonists to Veteran Soldiers is a good exchange).
Fourth, free land.
So just before the war of Independence, kill all Indians you can find - you will get money and colonists, train your soldiers, and avoid problems with the Indians.
A very important thing is that after you destroy an Indian capital, they become calm again. So if you plan a war to get more territory, destroy all small villages you want first, and only then their capital.
Trade with Indians
If the Indians live near some other power, are at war with them, and live far away from you, selling horses and guns to those Indians will not only gain you money but potentially weaken your opponent(s).
But always think twice about that - it's like giving weapons to Afghani mujahedeen for them to fight the Soviets. Even if they actually harm the Soviets, won't they use it against you later? What if you decide to assimilate those former Soviet lands? ;-)
After some experimenting I found that Indians usually get enough guns and horses without your help, and the ratio of harming your opponents to guns/horses sold is relatively small. Still, they'll pay you a lot (prices in the 500-1000 range are usual, unless they already have too much), and you may consider harming the other powers an added bonus.
When you send a scout to a village (which is a good idea, because of the monetary gifts you can get), remember to write down what they want, what are they selling, and what skill you can learn there. If you don't note it and need that information later, you may waste precious scout time reacquiring that information.
Sell them trade goods, maybe tools, buy silver, cloth and coats. And sell them the stuff they want/need, if you happen to have it and they pay better than Europe. Trade with wagon trains: Indians don't like trading with ships. Price negotiations can be risky but very profitable (some people will surely do this with the save/try/load/try again method). I don't like the way negotiations work in the game for that reason. If you want to buy as well as sell, send them a Wagon Train, and they will sell you as many tons as you sold them. If you use a ship, you will be offered only 1/4 as much as you sold them.
The Indians won't buy the same thing twice in a row, so you may think about alternating between 100 units of something profitable (tools and trade goods) and 1 unit of something else they want, even if you're selling at a loss (cloth, coats, rum).
The whole Indian business is just some extra money - maybe even quite a bit of extra money, but it's not going to be your main source of revenue.
The easiest way of transporting treasures is to get them to the coast, set a temporary colony with a scout or a soldier, have the king transport the treasure for you, and disband the colony. After Cortes it's free. If you don't have him you will just pay the transport fee, as you don't have any other option.
Moving the treasure all the way to your colonies is a huge waste of time, and there's a substantial chance of it being attacked by the Indians, even if it is escorted.
If you have a Galleon, the king won't offer you transport, so send it to get the treasure (no need for a temporary colony).