I'm not sure if anyone has written about this before.  I figured I would share with you guys the way that I study. Maybe it will be interesting for someone else.

First of all, let me explain why I made this modification.  I started Rtk 1 and I did it for only 2 weeks.  I was amazed at my retention rate with the help of the stories in the book and this site.  The only 3 things about rtk1 that I didn't like was the fact that even though I was learning the kanji, I couldn't really use it bc I was lacking the grammar aspect of  Japanese.  I did it. I broke the rules and I am currently learning kanji and grammar at the same time, but that is besides the point...

The other things was that I didn't want to have to go back and negotiate my memory of the english sentences that I wrote and replace it with the onyomi /kunyomi readings. It seems like twice the amount of studying.

The third thing was that some of the kanji in rtk is not commonly used ( and a lot of them are only seen in compounds, not stand alone). I didn't want to waste time learning useless information.

So, After about 2 months of focusing on writing and vocabulary I have decided to go back to learning kanji. I felt like I would save time if I learned the kanji with the readings at the same time and  I would be making visible progress in a timely fashion.

My method:

I got a bunch of kanji games for my ds but the main one I use is Tadashii Kanji kakitorikun. I have decided to break up my studies by grade level bc that's how the kanji are organized in the game.  Aslo, if I ever take the jlpt all of this information will be on par with the different levels of the test.

Essentially, I replaced the kanji from the rtk book  with the kanji learned in Japanese schools, by grade levels. This way, I know that I am learning kanji that I will see frequently.

Tadashi Kanji kakitorikun Kanji:
1st grade 80 kanji, 2nd grade 160 kanji, 3rd grade 200 kanji, 4th grade 200, 5th grade 185, 6th grade 181 kanji, 7th grade 316 kanji, 8th 286 kanji and 9th grade 337 kanji=
(1945 kanji total) So the numbers are close to rtk.

The advantage to using this game is that it also has a drill section, which is sentence drilling. You fill in the blanks with the kanji for reading and writing practice.

My anki Flash cards w/ mnemonics:

The kanji is on the front and all other information is listed on the back such as english meaning, yomi, radicals and then the sentence.

note: I break each kanji down to the radicals like hesig does but I only use the radicals in my phrase if I cannot think of english words that mimic the yomi readings. See examples below.

For each kanji I write a story but instead of using the stories in rtk I incorporate a sentence or phrase that contains either the onyomi or kunyomi ( or english works that will trigger the Japanese readings)

Ex. kanji:　夕
sentence: ”Can I see you this evening (meaning of the kanji -evening)?”
(kunyomi reading-ゆう）(meaning of the kanji -evening)
So when I repeat this sentence, I will instantly remember that the reading is ゆう and it means evening.

Ex: kanji: 見
radicals:　eye, legs
sentence: " I can see your legs."
*kunyomi-miru (meaning of the kanji-See) Here, both radicals are used in the phrase.

As for how many of these I learn a day, I started with 20 kanji a day so i will probably continue doing 20.

Let me know what you guys think about this. I'd be interested in getting feedback.