Do we know how these wars were waged, went, were settled? Before europe came and started colonizing I'm pretty sure there were conflicts between tribes but to be perfectly honest (even being a decently big history buff) I've never explored the subject.
How did they fight each other, what did they fight over? Did tribal affinity even really matter on a grander scale?
Re-re-posting from a similar question a couple months ago for an extra layer of saving time:
Rather than re-type a lot of information I've discussed elsewhere, I'll just point you to the rabbit hole and send you tumbling into an Iroquoian Warfare Wonderland. The post linked to discusses the war between the Haudenosaunee (the Iroquois Confederacy) and the Erie confederacy in the 1650s. The follow-up post there contains links to additional posts concerning tactics and equipment (with siege tactics being mentioned in yet another link), Iroquoian politics with a bit about how it influences war, and the fate of war captives. There's some bonus material sprinkled through out on other peoples like the Chickasaw and early colonial Mississippians. Enjoy, and if you have any follow up questions feel free to ask them here rather than scattered around in those old posts.
I would recommend a book like War Paths, Peace Paths: An Archaeology of Cooperation and Conflict in Native Eastern North America by David Dye (2009). It is the first book-length overview of the topic for Eastern North America and summarizes many of the issues.
In short:
Yes, violence was present in the indigenous Americas. We know this from the presence of weapons, skeletons showing the effects of violence, iconography and rock art, and fortifications. Interpersonal violence is, as best anyone can tell, a universal for humans.
The use of the term "war" needs to be examined. Scholars that look at violence across a lot of settings (agricultural/non-agricultural, state/non-state, large groups/small groups, strong leadership/less leadership, etc) often note that violence is organized in different ways, with different goals, and with different methods across these settings. There are sometimes broad similarities, and so folks like to be careful with their words and you will see terms like raiding, feuding, warfare, and others used to describe different expressions of violence. Lawrence Keely, Stephen Reyna, Ray Kelly, and others have developed and defined terminologies to help deal with these differences. For most of these scholars "war" has connotations that don't always fit with the types of organized violence presence among non-state communities, for example.
So what did they fight over? Dye, and others, have argued that for much of the last few thousand years most organized violence among native North Americans would best be characterized as "feuding" rather than warfare. Ultimate reasons could include territorial defense, vengeance, kin-group responsibility, and others. "Feuding" is contrasted against "war" in being more limited in scope and intensity, in being organized and prosecuted in a different way, and for having different goals for its participants.
Likewise, "tribal affinity" needs to be examined. The specific tribal communities most of us are familiar with are frequently by products of European contact (this is especially true in the eastern US). Clearly larger social groups did exist previously. In some cases they were simply defined by kin. In other cases they were politically motivated organizations of kin and extended kin, which is what one probably thinks of when they think of the historic tribes (Cherokee, Iroquois, etc.) The identities one subscribed to clearly would affect the kinds of motivations one might find acceptable for organized violence.
Dye would argue that before AD 1000, most organized violence in the eastern US is probably best characterized as "feuding." By AD 1000, in parts of the eastern US and midwest, there were political entities large enough and organized enough that Dye and others have argued it is appropriate to describe the organized violence they engaged in "warfare." Some of this warfare would be for the expected reasons, such as territorial defense, avenging wrongs, and to force tributary relationships. Some of the motivation might also be internal. Success in warfare could be a way for young men to gain status and for leaders to demonstrate their prowess.
When the Spanish explorer DeSoto traveled through the southeast in the 16th centuries, they got involved in lots of violence with the communities they encountered. Sometimes they worked with allies against another group. From that, we can see that the motivations for violence included (1) establishing or abolishing tributary relationships between communities or chiefs, (2) sacking and desecrating another communities temple, and (3) gaining some captives, and (4) when times were tough, taking food.
The arrival of the Europeans quickly and drastically changed the nature of warfare in native North America. The introduction of firearms rapidly created huge military advantages for those with them. The introduction of trade, such as for furs and skins, created a much keener interest in territory than had existed previously. The introduction of the Indian slave trade created an environment for total warfare that was probably extremely rare prior to this. And finally, the introduction of diseases and increased warfare created incentives for forming larger collectives of communities who needed to organize themselves for defense. For all of these reasons, we need to be extra cautious about applying what we know about post-Contact warfare to pre-Contact Americas.