It can be overwhelming to browse through books and websites, as many authors purport to know the "right" way to train a dog. As you will learn, however, there is no one right way to train a dog; as long as you are a responsible, loving, and positive puppy parent, there are in fact many ways to deal with common puppy issues.
When looking online or in the bookstore for supplemental training material, here are some trainers/authors you can trust: Ian Dunbar, Karen Pryor, Patricia McConnell, Jean Donaldson, Pat Miller, Turid Rugaas, and Teoti Anderson. Conversely, generally speaking, stay away from any books or websites that use the following terminology or equipment: alpha dogs and alpha rollovers, dominance, corrections, electronic, prong, and choke collars, and exhaustion training. For a quick article debunking the dominance myth, check out The History and Misconceptions of Dominance Theory by Melissa Alexander.
We've read just about everything there is on the market, and can confidently recommend the following resources for all puppy parents:
Excellent puppyhood books...
Before and After Getting Your Puppy by Dr. Ian Dunbar
The Ultimate Puppy Toolkit by Peggy van Dam and Sydney Bleicher
Quick and Easy Crate Training by Teoti Anderson and Stephanie Fornino
Way to Go! by Patricia McConnell
Your Outta Control Puppy by Teoti Anderson
Raising Puppies and Kids Together by Pia Silvani and Lynn Eckhardt
Excellent books on understanding dogs...
Don't Shoot the Dog by Karen Pryor
The Power of Positive Dog Training by Pat Miller
The Other End of the Leash by Patricia McConnell
Excellent books on clicker training...
Click For Joy by Melissa Alexander
Clicker Training for Dogs by Karen Pryor
Excellent books on fearful dogs and separation anxiety...
Help for Your Fearful Dog by Nicole Wilde
Help for Your Shy Dog by Deborah Woods
I'll Be Home Soon by Patricia McConnell