do i have to know witch one is kun or on reading?
Yes you should do that.
What i do is look up the stroke the order in an online as well as an offline(book/dictionary).
I use http://lingweb.eva.mpg.de/kanji/ its german, but there should be some similar english source somewhere out there.
I am also using this: http://www.amazon.com/The-Kodansha-Kanji-Learners-Dictionary/dp/4770028555
There is also an IOS version: https://itunes.apple.com/de/app/kodansha-kanji-learners-dictionary/id512864153?mt=8
I tried the book "Remembering the Kanji" but its not for me.
What i do is:
- learn vocabulary -> take unknown kanji from this words
- look those kanjis up in a dictionary (for stroke order, readins and further examples)
- create a paper Flashcard with the information gathered
- do srs with those Flashcard
What really helps a lot is if you learn the Kanjis with example Words, sentences ect.
Learning Kanjis just for the sake of knowing them is not very benificial and won't really help you to read.
The more Kanjis you know, the easier it becomes to learn new one (at least in my opinion). There will come a point where you dont need to look up stroke orders any more, cause you can tell what a Kanjis stroke order is simply by looking at it.
You will also notice familiar patterns from other Kanjis which will make them easier to remember ect.
I am learning 1-3 Kanjis per day with this method. Its kinda slow but steady but i can "use" the Kanjis i learned like that.
If you really want to use "Heisigs" Methods, i think its best jsut to use as an additional source, but NEVER as the main source for learning Kanji.
Hope this helps a little.