Email based workflow is included in the Database Accelerator for specifically this type of scenario. Qdabra Database Accelerator Suite Version 2.0 - Developer
Otherwise, yes, you could have two forms but you would need a database to share the data in between the seperate forms. Data is stored as an InfoPath document in XML format, so each one is a flat file like a word or excel document. The template you design is the template used to organize the data and control the completion of the form.
In similar HR forms in the past I have done both, I have created forms that are very complex and have one view for Managers and one for Employees, I also have used multiple forms and kept the data in a central database. Each of the scenarios is less than ideal for an enterprise solution becasue they can be circumvented and or tampered with. The problem is that for sensitive employee data such as performance appraisals, you want to ensure due diligence and make sure your process is controlled and secured and that you have an audit capability.
The way to do it right today is to utilize the Database Accelerator. Then you can migrate all of your HR forms to electronic and have one consistent, packaged method for controling and securing them. It is inexpensive and much easier from a development standpoint since all of these tools are at your disposal out of the box.