I also study with vocabulary that I usually find from my Japanese shounen manga collections.If you don't have access to such things, Pulling words out off Wikipedia articles is also helpful.
I don't even read the manga until I've learned all the Kanji words.
The way I study is by using a SRS (spaced repetition system) flashcard program like Anki, in front I put the Kanji with the reading next to it and on the back, the English meaning.
I study about 100 different words everyday this way and don't usually learned them until it goes to my long term memory so when I do master them, I go back to the manga and I begin reading without pausing.
I would usually understand what I am reading because I've learned all the words.
There is an app called 漢字ドリル
It was really useful for me Just do the drills a lot .
Here you can find essays for every grade that cover all the kanji learned in that grade
you can also start reading.. and reading a lot.
for free reading try hukumusume it is a site with a lot of stories.
You also can find and use the mobile application (besides the books).
I used application like, "Memrise" for studying Kanji. ^^
And you must remember, DON'T LEARN KANJI JUST BY READ IT OR SEE IT ONCE (OR MAYBE WRITE DOWN ON YOU NOTEBOOK).
You must reply to write it everyday, write and write and write.
When you write down one word, you must also spell it on your mouth. When you write and read it, you will be able to remember it fast.
Don't forget to remember the meaning too. ^^
Hope this can help you.