Since iMovie doesn't have a setting to set a folder inside the drive and stores things at the root of an external drive, you can use folders to segregate projects quite nicely.

When you open iMovie, just right click on the name of the external drive and make a new folder. Make a second folder and name them for each of you. When you open iMovie, you can collapse her folder and vice versa to avoid having to see all of the projects for the non-active user.

You could also make disk images on the drive and store them anywhere, but that is a bit more tedious for little additional payoff. You would avoid having two folders made at the root of the drive, but at the expense of a more complicated storage layer. The down side is you still have folders at the root of the external drive as well as all the project footage is in subfolders rather than in their own folder.

The remedy for this is to create sparse disk images for each set of projects and mount them before moving content to each "disk". The iMovie visual will be as if you have two drives additional drives even though they are just files/folders on the same drive.

The only warning I have is when you have multiple clips referencing the same footage - avoid moving one and not the other. Moving all the projects to the external would be extremely robust and workable, but iMovie can be a little too aggressive in moving footage to a new drive without checking to see if other projects left behind reference that footage. Luckily, things re-link nicely once you discover the missing footage error and reunite the "left behind" project with it's partner and footage.

For apps that don't support two-factor authentication, such as iMovie, you need to generate an application-specific password. This is a computer generated password that can be used to give an app access to Google services, but is intended for use in a single app.

Go here to manage your connected apps and application-specific passwords. Once you generate one (be sure to label it as "iMovie password" or similar), copy it into iMovie making sure to use your full Gmail address as the "Account Name", then you're done with it.

There's intentionally no way to view the password again, the only possible action is to revoke it. This way your account still stays secure as long as the app stores the password securely (and if it doesn't, you can always revoke that one password without causing problems for the rest of the account).