The first thing I want to stress about learning kanji using the RTK method is speed. Speed is important because your motivation decreases with time. If you go too slow, you run the risk of losing your motivation before achieving any significant target (e.g. a nice round number of kanji learned) that would give your motivation a boost. Then you'll quit. And once you quit, you'll forget everything you've learned. And then you'll have to start from the beginning the next time. So once you start, it's important to go fast. My suggestions below are designed to maximize speed more than anything.
1. Anki. This is spaced repetition software (SRS). You will want to use this extensively when you want to memorize anything. SRS is a significant breakthrough that optimizes memorization significantly. I don't want to write about the theory behind SRS right now, you can google it yourself. But trust me, an SRS tool (I recommend Anki) will be indispensible at every step in the process of learning a language. So this is where you get Anki: http://ichi2.net/anki/ Watch the intro videos on how to use it. Once you install the app, download the Japanese plugin to enable Japanese support. Then download the shared Heisig RTK deck. You won't have to enter anything, everything is already premade for you.
2. Get the kanji stroke order font here: http://sites.google.com/site/nihilistorguk/ (first link). The picture there shows you what it looks like. Install the font in your system. Open the Heisig deck in Anki and set its properties to use the kanji stroke order font to display the kanji. Also make it big (like 100 points). You need this so that when you test yourself, you can also easily check if you got the stroke order right.
3. Register on this site: http://kanji.koohii.com/ It's called Reviewing the Kanji or RtK for short. This site is designed as a companion to Heisig, and it includes its own SRS and a way to manage and share stories. Anki is superior as SRS, so you should use that. You should use this site for stories.
Don't bother coming up with your own stories. It takes too much time. Pick the best story that someone else has already come up with on RtK. In 99% of the cases it will be better than what you can come up with on your own anyway, and much quicker. For some reason, the ones involving sex and/or extreme violence work best.
Incidentally, Anki Heisig deck is already set up to link to the RtK site when you click on a keyword. So when you pick a story you like there, click a button to copy it into your own story (the site, if you haven't seen it yet, allows you to write and maintain your stories for Heisig), and you can basically refresh your memory with one click of a mouse button in Anki.
Don't bother writing kanji on paper. I started doing that, then I stopped in order to save time, and there was no significant effect at all. I basically trace kanji with my finger on the desk. Works just as well. If you want to practice writing kanji, you should wait until you complete RTK1 (don't let anything unnecessary slow you down until you complete it), get some genkoyoushi and practice on it. You can just write all 2042 kanji from memory once if you want, you'll need about 11 sheets I think. It's difficult to keep kanji to a square shape if you're not doing it on graph paper until you've practiced enough.
So here's the system I ended up with toward the end of my RTK1 studies, and it's the one I would've used from the beginning if I had to do it over. Also I will use it once I decide to do "Remembering the Hanzi" series.
1. Study one whole chapter at a time. The only exception might be for several huge chapters, one had 130 kanji, the other 96, and I think there were some in the 80s. That's really too much for one sitting. In that case, split on primitives. Study up to a certain primitive. Don't study kanji involving the same primitive on different days.
2a. Read the whole chapter. Heisig provides stories for the first 600 kanji. So in the beginning you read everything including the stories. Trace each kanji and each primitive that doesn't have its own frame number on the desk with your finger as you read. Just once.
2b. When Heisig stops providing stories, you can start relying on RtK stories (or you could do this for the first 600 kanji as well). In this case, you scan the chapter in the book to see if Heisig has any special notes for a kanji (he usually doesn't) and just to get an idea for the scope of work in front of you. After that, go to the site in the study section, and for each kanji in the chapter pick a story you like best. Again, trace the kanji with your finger just once.
3. After you've studied the chapter, go to Anki and add that number of new kanji for study. It will go through the keywords, and you try to trace the kanji with your finger while *counting the strokes*. After that, make sure that the number of strokes matches, and that all primitives are there and in correct positions relative to each other. If that's the case, pass the kanji, if not -- fail, and do it again in 10 min (that's the default setting in Anki). When you pass a kanji for the first time, choose 'Hard' so it gets scheduled for the next review on the next day. If you don't take a long break between studying the chapter by getting the stories down in your RtK profile and doing it in Anki, you should pass at least 80% of the kanji initially. The KanjiStrokeOrders font you can install on your system comes in handy here. That's because Heisig also eventually stops giving you stroke orders, and sometimes you really don't know what the correct order is.
If you have study time left in the day, repeat steps 1-3 with the next chapter, etc.
4. The next day, first review your kanji backlog, then start from step 1. You might find that you've completely forgotten half the kanji learned the previous day, and half forgotten another quarter. Not a big deal, it's normal, don't let it discourage you. Fail them, review after 10 min, say 'Hard' again to schedule for the next day.
Finally, when you're about 300-400 kanji away from completion and feeling sick to death of Heisig and kanji in general, you need to make one last push to put the whole ordeal behind you. At that time, I would recommend that you abandon reviewing the backlog and just study new kanji. Try to reach 100 per day. After you've studied the Sign of the Snake (which will become your favorite kanji ever, because it's #2042
), you can start dealing with the backlog over the course of the next week (my backlog on the next day after I finished was over 500 -- obviously, I couldn't work my way through it in one day, I think it took me two more days to catch up). Reviewing something you've already studied is much quicker than studying for the first time, so it should really be all downhill from that point on. Two weeks after completion my reviews were down to ~100/day, which took me about 20 min to go through. I still failed some kanji, but only 2-3 per day at that point, and I didn't need to look up any stories because I would remember them as soon as I saw the kanji.
I think that for someone who doesn't have a full-time job it would be possible to do 100 kanji per day consistently, which would let them complete RTK1 and be left with just reviews in only 20-21 days. Well, I did it in ~50 days. I think my memory is pretty good, but not the greatest. So I don't really see anything amazing in this speed. Try it out, everyone is at first amazed how easy Heisig's system is, at least until the backlog of kanji reviews starts snowballing.
One last warning. Most people say that there are two points in RTK1 that make them quit (or almost make them quit). Somewhere after 600 kanji and somewhere after 1200 kanji. I think I only experienced the pain after 1200. But I was really on the brink of quitting. I hope that armed with this knowledge beforehand you will be able to get over those two dangerous points without quitting.