How can I include a shaman as a bad guy for a run that the players need to deal with. Where can I read about Shamanism and their role in the setting?
My Shadowrun experience is mostly 1st and 2nd edition but I don't think the fundamental idea of a shaman is that different in any edition of SR.
In Shadowrun a shaman is, traditionally, defined by their totem. The totem heavily influences the personality and drives of most shaman. Some would say the totem shapes the shaman and others contend that the shaman is drawn to the totem that fits their "true self" best. There are countless origin stories of shaman that support one camp or the other. The end result is the same, shaman and totem spirit are of like mind. So pick the totem accordingly.
If you want to use a shaman as a foe pick a totem that fits. It doesn't have to be that this NPC is "evil", it could just be their goals are mutually exclusive with the goals of the party. This can even work out to be more dramatic as, from a certain point of view, the goals of the NPC can be understood. So, for an urban shaman I'll go with a Dog, Raccoon, Rat or Raven. All of them will do well in a city and make excellent foes but not necessarily evil foes. Dog is very loyal and a true defender, imagine being on the wrong side of a Dog shaman. They don't give up and will not stop coming for you. Raven would be fun too. The motives of a Raven shaman could be very mysterious. In some cases they have none, it was all just done for the fun of the game or as misdirection as Raven strikes in another direction. And if you really want evil it is hard to beat the Spider totem, such a shaman is a mastermind, plans within plans having counter plans with backup plans. Also, if there is an SR4 variant of the toxic shaman that will really cause the PC's trouble. The toxic spirits of the cities are twisted creations full of all the foulness better living through chemistry can create. They are brutal and brimming with rage.
As to how the Shaman fits in with the world, think about it like this. The clash between old and new, magic and tech, the rational and the spiritual are heavy influences in the world of Shadowrun. That was kind of the point with having a world in which magic and tech stand side by side. While Shadowrun looks like a high tech, future world setting it is much more. It is a world that embodies the duality of the human experience. The comfort of what is old and has always been next to the trill of new creation. That is magic and tech. Friction.
That said it should be noted that not all Shaman are Luddites. Shaman will use tech, some more than others. That seems to be influenced by the person's life before hearing the call of their totem. And some totems have less problem with it in general. Take Raven for instance, the spirit is a classic trickster and may well find some forms of tech to be fascinating and rife with possibilities for entertainment (tricks). Fox may use tech at a critical moment just because the opponent would not expect it. On the other hand a shaman of Eagle will be one of the least likely to ever use tech of any type.
While Shadowrun:Denver is mostly 3rd edition it is the most expansive Shadowrun repository I have found. It has a section for fiction that has some stuff you may want to read. The log section may be entertaining as well. There is a section for...everything. Go and check it out, you may spend days reading.
If you have the time to read some of the Shadowrun novels do so. They can do wonders when it comes to helping you get a feel for the world.