Does anyone know of a site or book that shows how to properly write the extended hiragana and katakana, such as kya, kyu, kyo, and gya, gyu, gyo and di, dyu, etc?

Any other information or advice is appreciated as well. Thank you.

The extended Kana are just a combination of Kanas, so the order of the strokes doesn't change, if that is what you are worried about. If you are not sure, how a special Kana is written, go to this website: http://www.umich.edu/~umichjlp/Hiraganapro/

If you want to test yourself, this is a good website (although in German, but you don't need any to understand how it works): http://www.unckel.de/kanateacher/

Didn't use it to learn kana because I didn't know it back then, but the kana section of Kanjibox (http://kanjibox.net/), that you find setting your level at JLPT5 seems quite good for testing yourself.
It also use some more rare katakana combinations (like フェ or　ヴぁ) which you won't normally see in hiragana since are mainly used to phonetically write foreing names. If you practice a bit on that website you should be able to write any sound without really have to think about it.

Thank you both for your posts. I'm definitely going to check those sites out.

It also helps to know that the stroke order is the same. I was just mostly curious about the smaller kana symbol and whether or not it was written after the first larger kana symbol, and also whether or not that applied for both hiragana and katakana, or if there was some change in the rules.

It makes sense that it would, but I'm mostly just confirming things for myself so I don't somehow develop an incorrect writing habit.