I don't have the time to get to all your questions right now, but I thought I'd start with one part and, assuming no one else beats me to it, come back and provide more cultural details and book recommendations about at least some of these later.

Who were they?

• The Wabanaki Confederacy: This is an alliance of the Mi'kmaq, Maliseet, Passamaquoddy, Abenaki and Penobscot. They fought alongside the French (or more to the point fought against against the English-Haudenosaunee alliance, which were also enemies of the French).

• The Wampanoag Confederacy: This was the nation that allied with the Plymouth colony. In the 1670s, they gathered additional allies, including the Nipmuc and the Narragansetts, and fought against the English in Metacom's War. While they actually had a technological advantage (most of the colonists were fighting with older matchlock muskets, while the Wampanoags had previously acquired newer flintlock muskets through trade), they had a sizable numerical disadvantage and eventually lost that war.

• The Pequots and the Mohegans: These were originally once nation based in what is now Connecticut. They split over European alliances, with the Pequots siding with the Dutch and the Mohegans siding with the English. The resulting Pequot War was devastating to the Pequots, as the English campaign against them became genocidal. The Mystic Massacre is the most famous incident in that war.

• The Lenape: At the time of contact with Europeans, the Lenape were a large collection of autonomous communities. They wouldn't have a unified political structure until the 1700s, by which time they had relocated to what is now eastern Ohio. The people who "sold" Manhattan to the Dutch were a Lenape community. During the colonial era, different Lenape communities traded with the Dutch and Swedish, and later the English. They're most fruitful European relationship was with the early Quaker settlers of Pennsylvania, as their leader William Penn worked hard to form fair and equitable agreements between his people and the Lenape. Unfortunately, that good will didn't last long and by 1737, the Lenape in Pennsylvania were swindled out of a sizable amount of land during the Walking Purchase. Around this time the Lenape were integrated as non-voting members of the Haudenosaunee, and it was to the Grand Council that they appealed the Walking Purchase. The Grand Council rejected their appeal and granted them land closer to the Haudenosaunee heartland in New York. Eventually, they were given a larger amount of land in Haudenosaunee-controlled Ohio.

• The Haudenosaunee: Also known as the Five Nations (from east to west: Mohawk, Onedia, Onondaga, Cayuga, and Seneca) or the Iroquois, the Haudenosaunee are an old and powerful confederacy based in what is now upstate New York. They developed long-standing alliance with the English known as the Covenant Chain. During the colonial era, they expand their influence westward rapidly to the Mississippi. I'll quickly note the Susquehannock here for a moment as well. They were another Iroquoian confederacy based in central Pennsylvania. Early in the colonial era they were allies of the Swedish, but by the time the English colonists came into the area, they had been integrated into the Haudenosaunee.

• Tsenacommacah: This is one of the most famous Native nations during the colonial era, but the name is most likely unfamiliar to you. Your probably know them as the Powhatans, which is actually the "throne-name" of their leader at the time Jamestown was settled (a name he chose to recall the original capital, formerly located near Richmond before it was moved to Werowocomoco. You probably know of Pocahontas (who never had a romance with John Smith, despite what folk history will tell you), and her father, the mamanatowick Wahunsunacawh (aka Chief Powhatan), who made an uneasy alliance with the English. Some other prominent Powhatans include Don Luis, who was abducted the Spanish decades before the English arrived as was taken to Florida, Mexico, and Spain before returning to his homeland to help establish the short-lived Spanish colony of Ajacan (short-lived because Don Luis organized a counter-attack against it before it could firmly establish itself); Uttamatomakkin (aka Tomocomo) who was Wahunsunacawh's son-in-law (married to one of Pocahontas' half-sisters), a prominent priest of the Powhatan religion, and an explorer dispatched to England to gather information about the size of their population and the state of their resources; Opechancanough captured John Smith and was the leading voice in opposition to English colonization, eventually leading two anti-colonial wars during his time as mamanatowick; Cockacoeske was Opechancanough's daughter and the last mamanatowick of a united Tsenacommacah, after her the territory was divided up by the English and a proto-reservation system was established. I should also make a quick note here of a neighboring nation, the Piscataway, who had a similar political system north of the Potomac River.

• Tuscarora: The Tuscarora are an Iroquoian people from North Carolina during the early part of the colonial era. Unfortunately, the Carolinas were a bad place not be European during this time, and as the slave raids against the Native people of Florida started to dry up in the early part of the 1700s, the Tuscarora became convenient targets. Their resistance to the slave trade and their eventual flight north to seek asylum with their Haudenosaunee allies is known as the Tuscarora War. They eventually became the Sixth Nation of the Haudenosaunee.

• The Catawba: That map is a Catawba-made of their territory and their neighbors. The circle in the center is Nasaw, their captial. You can also see Charleston, SC on the map, as well as Virginia, the Cherokees, and the Chickasaws. They were based in western North Carolina and northern South Carolina (hence the Catawba River]. Until now, all the people I've mentioned have either been Algonquian-speakers or Iroquian-speakers. The Catawba, however, were the principal Siouan-speaking nation in the east (there were others like the Tutelo, Saponi, and Monacan). The Catawba were one of two major southern enemies of the Haudenosaunee, until the English colonists helped negotiate a peace between the two nations (conveniently securing access to the major pathway between the two nations).

• The Cherokee: The Cherokee are distant Iroquoian relations of the Haudenosaunee and for a time they two were enemies (as you can see on both maps, for a time they were both vying for control of parts of Kentucky). They eventually settled on the Ohio River as their border. Like the Lenape, they were originally a collection of autonomous communities, but over the course of the colonial era they became increasingly centralized. Shortly after the American Revolution, they adopted a similar Republic-style government as the US.

• The Creek Confederacy: This confederacy developed out of the ashes of De Soto's entrada in the 1500s. As the old Mississippian polities broke up in the chaos that followed De Soto, a new political system emerged based around regional collections of towns (most prominently the Upper Creeks and Lower Creeks). This was a multi-ethnic confederacy, but the dominant group was the Muscogee. Early in the 1700s they participated in the Native slave trade, joining the Carolinian English on raids into Florida; however, they also became a prominent refuge for escaped slaves later in the colonial era, who became members of their society. Like the Cherokee, the Creek Confederacy began to develop a Republic-style government after the American Revolution, but it met with considerably more resistance. The main proponents of adopting an US-like government were seen as self-serving sell-outs. The conflict spun out into a civil war, resulting in the Creek - Seminole split.

• Native Floridians: I'm going to lump the pre-Seminole Native peoples of Florida into one entry here. The main interaction English colonists had with them was in the form of slave raids conducted by the English and their Native allies. Thousands of Timucua, Apalachee, Calusa, etc. were removed from Florida every year and sold in Charleston slave markets, most bound for plantations in the Caribbean.

EDIT

• The Yamasee: Based in South Carolina, the Yamasee were another multi-ethnic confederacy like the Creeks, with whom they were allies. They also aided the Carolinians in their slave raids into Florida and against the Tuscarora. The Yamasee get top billing in the Yamasee War, which is a misnomer, as discussed in this post.