The Drumming System has a good amount of exercises to help you develop bass drum independence. It suggests playing everything heel down at first, then heel up, then heel toe. Eventually, you won’t have to think about any of this when you play.
As a supplement to the Drumming System, I have found the following books very effective for developing independence:
Bass Drum Control by Colin Bailey – The book starts off with some simple, but effective warm-ups for developing rhythmic control and accent control with a single kick pedal. After that, the book goes into hand and foot patterns that will challenge you. TIP: Play quarter notes with your foot on the hi hat while playing everything in this book. You will really develop balance, timing, and independence.
Bass Drum Control Solos by Colin Bailey – Learn how to incorporate the bass drum into your drum solos. Fun!
Rockin’ Bass Drum by Charles Perry – Learn some of the most popular rock beats. TIP: Practice doing the beats in this book with different cymbal patterns. For example, you can play the beats while doing quarter notes, eighth notes, sixteenth notes, etc.
Rockin’ Bass Drum, Book 2 by Charles Perry – Part of me believes this book is over the top. You get to play some challenging beats. Some of them just seem unnecessary (that just my opinion). Regardless, it will get you to push yourself one step beyond the first book.
In addition, the are some good exercises in the Drummer Essentials eBook, which you get for FREE when you sign up for the FREE Video Drum Lessons on this site.
As always, be sure to use a metronome while practicing.