Phrasal verbs are either separable or inseparable - a learner's dictionary* will tell you which ones. If they're inseparable, the verb must stay next to the particle. If they're separable, the object can come between the verb and the particle or after the particle - but not if it's a pronoun. So your 'unseparated' sentences are wrong:
Write it down.
Write down it. But you could say "Write down the sentence".
Note it down.
Note down it. But you could say "Note down the sentence".
PS * At least, a decent one will. Don't waste your money on one that doesn't give this sort of information.
- For Teachers