So how do I use them? I'm glad you asked! Oh, you didn't. Well, pretend you did :-)
I do basically the same thing I was doing in The Ordinary Parent's Guide except I'm introducing things in a slightly different order. I started this on my own but then found Brandy's Teaching with Bob page and that was very helpful. I suggest taking a look at it if you are using the Bob Books even if you change things up like I am.
I started out thinking I'd do it in advance and type them up so they'd look all pretty and quickly realized that was silly. This takes about 2 minutes of my time and I just keep the sharpie is our basket so I can add them in a second if I accidentally miss one, which has been known to happen.
My basket of gear - the opposite of complicated
After we learned any new sounds, we'd do a bit of review. Lucy prefered to review exactly seven from each category so I would pull the front seven green/blues and the first seven pink. Instead of using Brandy's neat binder system, I put them back up in a way that facilitates needed review. It's not as fancy as it sounds - if she got it right quickly, it went to the back of the pile. If she hesitated, guessed or gots it wrong, I put it back at the front of the pile so it got included in the next day's "seven." This was all done without her even knowing it so she didn't feel penalized if she got it wrong, I just keep my finger between the stack in my hand. Every once in a while I would go through and pull the ones I knew she really had down so our pile was never huge and we could work through them all in 3-4 days. That way we never went too long between reviewing any one word or sound.
We just finished Set 5 about a month ago and honestly, that last book was a bit of a struggle. It's an odd book (she clanged the clong? Really?) and I could tell Lucy just didn't care about the story so it took us 4 days . But in other books, she took off. She went from sounding out almost every word to just, well, reading! So for now, we've dropped the index cards and are just reading for about 10 minutes a day, either from the Treadwell primer (free online) or the Pathway Reader Primer (passed down to me by my mom). Since I have and like both sets, we are skipping back and forth. She's also started to enjoy easy readers from the library and some of our picture books (although those are a bit harder for me to gauge her on since she has a lot of them memorized already!).
I did look though the Ordinary Parent's Guide to see what rules we've covered and which we haven't. Between the Bob books and my pointing out other rules as we see them, she's knows most of them. And I have a good idea of the ones I need to keep an eye out for so I can explain them if we run into them during our reading practice time. But for now, I think we're done!