Hello @dreavisPH
In your excel file you could have 3 columns: Name, Primary Email, Secondary Email and do the following:
1) Get User in Azure AD with Primary ID
2) If the user is not found, it will throw an error, so you capture it and create the user with its Primary Email address.
3) If a user is found with the same Primary Email address, create the user with its secondary email address:

To capture the error in the "Create User - Primary email" you should do the following:


Hope it helps!
Ferran