It is possible to have separate accounts on the same computer. SpiderOak ONE keeps its application data, all the data regarding your account and devices, within the user profile. So if you're using two different user profiles on the same computer, you could make each of those different devices on the same account - or attach them to completely separate accounts. Being logged into your user profile will use your ONE account, and her user account will use hers.
If you've never used ONE on a particular user profile, the first time you launch ONE it should prompt you to either create a new account or sign into an existing one. Use the Sign In link, enter the username and password for the appropriate account, and then go through the process of setting up the new device on the account.
Once the device on that user profile is set up, you can swap between the two users and the appropriate ONE account will be used. The only caveat we might give is this: if you don't completely log out of one user and log into another, but instead just swap users and leave the second user logged in in the background, you'll have two iterations of ONE running at the same time.
They will not interfere with one another data-wise, but because ONE is very resource-intensive, you might see some system strain if both versions are running at once. I'd also make sure to not select for backup anything which isn't within the user's profile. If you do have to back up something not within your user, make sure it's only being backed up by one of your accounts - trying to access one file from two accounts at the same time could be problematic.