Yes, you can enter time for project purposes only, Graves. Ensure to add the time entries to the project.
Given that your exempt employees receive fixed salaries and are paid on specific dates each month, I recommend running their payroll first and then manually entering their time into the system. This way, your payroll stays simple and your project tracking and time management remain accurate.
To manually enter time, refer to this article for guidance: Enter your time in QuickBooks Online.
For future reference, scan this material to learn ways to trace expenses related to work made by your employees: Track hourly labor costs and profitability by project in QuickBooks Online.
You can always revisit this thread if you have additional questions about managing time entries or any QBO-related concerns. My team and I are always here to assist you.