The difference is between "in" and "into" is generally a matter of ACTION. I normally use "in" as a preposition (ex. "He is in the store"), but I use "into" to describe an action. For example, if "I went into the store", I was not previously IN the store, and now I have changed where I am by going INTO the store.
IN describes something that is holding still, something not moving or changing in any way.
INTO, on the other hand, describes something that has changed, some state of being that is not the same as it was before. "I turned INTO a monster", "I went INTO my house", etc.
Keep in mind though, that sometimes English speakers do use IN to describe an action. You CAN say "I went in the store", and it does not sound odd. IN can be used in place of INTO, but INTO cannot be used in place of IN. You can't say "I am into the store", but you can say "I went in the store".
I hope this helps :)