You are on the right track. Below is a screenshot of how you should approach your scenario:

1. Query Employee List - Get ALL employee numbers from your employee list and store them in a collection. If you have a large number of employees you might want to consider splitting them in batches to increase performance.
2. For each - For each employee in your collection, store the employee number (assuming this is your reference point in the timesheet list) and query the timesheet list for any entries matching that number
3. Run if - if the result of the timesheet list query is blank the employee hasnt submitted a timesheet
4. QUery Employee List - using the employee number, query the email or username from the employee list and store the result in a variable
5. Send Email - using the variable above, send an email to the employee reminding him/her to submit a timesheet
6. Set variable - in case the timesheet list query returned a result, you will have to reset the variable to a blank value otherwise the Run if action will never trigger as the result will be inaccurate

Hope that helps

Thanks that helps so much, I was just getting myself mixed up....