I move this to its own topic, but I think it’s a big discussion, and an important one!
There are three links on the QIIME 2 resource page, all of which I think are good starting places. The Coursera is video lectures, mostly focused on 16s, but they should give you some of the basics. I’m not sure about the current release cycle, so watch that.
I know Dan Knights also did a series of video lectures a few years ago. I think these should cover both marker gene and shotgun. However, as full disclosure, I’ve assigned them to students but haven’t been all the way through myself. (The video of him solving a rubix cube in 13s is pretty cool, too).
Numerical Ecology by Legrande and Legrande is kind of a bible in this area, but may be more complex than you want.
And, of course, feel free to come ask questions and/or share resources here.
I’m hoping others have suggestions as well, because this is a common question and not always an easy one to answer.