Way to go. Hope the site proves worthwhile to you.
Hm, the method I used isn't necessarily the "best" way but it seems to be the most frequently used practice from what I've seen - old-fashioned, repetitive writing. Sit down with a writing tool and paper and write the characters over and over and over. Tedious? Quite! Effective? It was for me.
I started with ひらがな(hiragana) and worked in sets, beginning with the "vowels" あ(a), い(i), う(u), え(e), and お(o). First, learning the proper stroke order of the syllables and the correct pronunciation of each. I do believe JPod101 have videos showing how to properly write each of the syllables and definitely have sound clips of the way they are pronounced. My kana learning actually came before finding JapanesePod, so that's why I sound uncertain if they have writing tutorials. Anyway, after writing and learning the "vowels" from numerous sessions, it was on to the 'k' column (i.e. か(ka), き(ki), く(ku), け(ke) こ(ko)). And then the 's' column, followed by the 't' column, and so on. As I wrote, I would say them out loud. To quiz myself, I made simple flashcards. Then, it was to do the whole process over again, but this time with the カタカナ(katakana) system.
漢字(kanji) is a different matter, and will take much longer to "master" compared to 'hiragana' and 'katakana'. Some suggest learning 'kanji' in context - learning them in words and remembering it in that form. Some also suggest instead of learning a 'kanji' and its multiple readings, you should focus on the general meaning of that kanji. For the most part, I agree with these suggestions, and personally, I'm using "Remembering the Kanji" by James W. Heisig to aid me in my learning, in addition to the tools on here, of course (do some research on Heisig's book if you like, it's not for everyone). But, as I said, kanji is going to take some time and because of that, I would say not to sweat it too much right now.
Primary focus should be on ひらがな and カタカナ for a while. Make sure you know those like the back of your hand, then you can worry about kanji. Good luck.