Applying to Language School and University separately – How does CoE work?

Hi everyone.
I've just recieved confirmation of a study abroad scholarship to Japan (private scholarship from Australia, not directly affiliated w/ Japan). In my study plan for the scholarship, I have 3 months language study followed by 12 months university study. These plans are immutable except in extenuating circumstances, so both have to happen.
How does getting a CoE work in this case? Do I need on from both institutions to get a visa?
Thanks