If she has a separate user account, what is done on that account is independent of what you do on your account. It is like if you each had your own iPhone. You can't have multiple accounts signed into an iPhone or iPad but you can on a Mac if each person has their own user account.
It isn't complicated (I have seen multiple accounts on computers for the past 30 years, both Macs and PCs, and I am just an everyday user) but I think you are over-processing this and that is making it appear complicated.
I haven't set up a separate user account on my computer (I am the only user) in many years but it wouldn't surprise me if when you set it up for her, you simply signed into your Apple Account in her computer user space. You now need to sign out of your account on her space and have her sign in with hers. You should both be there to do this since it will require your account information to sign out.
Read this document to learn how to sign out of iCloud on your iPhone, iPad, iPod touch, Apple TV, or Mac --> Sign out of iCloud on your devices - Apple Support
Read this support article to learn how to sign in with your Apple ID on various kinds of devices --> Sign in to your Apple Account - Apple Support
Now it gets a bit complicated since iCloud populated her user space with your information when you signed into that area with your account. When you sign out of your account from her user space (this does not affect your user space), it will ask you if you want to keep the data that are there. If this is purely your data, then tell it not to keep the data (meaning your photos, your contacts, etc.) If in the past you have been jointly using your account, you can elect to keep the data and she will have to sort through it all and delete the things she does not want. That's the only "complicated" bit.