The Arduino IDE provides a convenient way to write and upload your Arduino code. It also features basic monitoring of serial output from the Arduino board.
The Anaconda Python distribution contains the Python-based tools you need to build dashboards and analyze the data you acquire from your devices.
Fritzing allows you to make circuit diagrams and pictorial representations of your Arduino and breadboard.
The Art of Electronics by Horowitz and Hill is considered by many to be the book on building electronic circuits.
Getting Started with Arduino by Banzi and Shiloh is a good introduction to using Arduino for building electronic prototypes.
Programming Arduino and Programming Arduino Next Steps by Simon Monk focus on the software side of making Arduino-based prototypes.
Arduino Cookbook by Margolis, Jepson, and Weldin provides more advanced recipes for using Arduino.
Free instructional materials for electronic prototyping abound. You can often do well by simply Googling what you are trying to find out.
Arduino provides useful tutorials on their website.
The Arduino language reference is an invaluable resource to quickly look up the APIs for various functions.
The Arduino forums abound with tutorials, tips, and traps.
Adafruit has fun learning modules that can help get you started with electronics projects. They do not go into much technical detail, but provide a nice functional level of understanding.
Like Adafruit, SparkFun also has good learning resources.