[chryuop]

No just pay attention when you type through the IME. Usually the bigger problems are when you meet pair of letters like んに which turn out as んい or words where you have にや which turn out as にゃ. But I agree that writing helps you learn faster than typing.
Trust me after almost 3 years I still send in my written exercises with those mistakes LOL.

BTW, from what I hear, even native speakers use English IME to type in Japanese and not a Japanese keyboard.