The lessons which show you how to draw the kana (hiragana and katakana) with stroke order attempt to show you how to write them in the correct handwriting. A perfect example is the hiragana for き. In "print" form, you see the last two strokes connected. However, in handwriting, these are separate strokes that have some spacing between them.
Pay attention to the stroke orders to correctly identify how to WRITE the kana. Japanese people will still understand what you are writing, it will just seem a little "off". And stroke orders are very important in order to avoid bad habits as you start to learn to write Kanji (where stroke order is very important).
If you want EXTRA practice on how to write, Nihongo Master has practice writing sheets for hiragana, katakana and for almost every single kanji in the dictionary. This feature is available to Premium Members and allow you to print out the pdf. Each pdf has the stroke order for the items you want to practice, as well as plenty of practice spaces for you to try it out yourself.
Good luck with your studies!