Hi CMartinKo and welcome,
You can map your forms to a list and use that to aggregate information on employees. To map form data to a list, you need to promote it to SharePoint form library (form options->promoted properties). Then, you create a workflow to add items to a list. We demonstrated this in our weekly webinar on June 27th. See the metrics list towards the end of the 30 minute webinar on youtube.com/Qdabra).
Another option is to map the data to the list on submit using CAML or qRules. We've webinar'd this quite a lot recently including August 15, February 28, and March 7th. Here is a page that has links to these webinars: http://www.qdabra.com/en/training/trainingvideo.aspx.
You could also create a dashboard form using InfoPath designer that queries your existing InfoPath form libraries and aggregates the data in a view. Such a form could be published as a dashboard - in essence, it's a web page design tool and not a data collection form. We've demo'ed this concept quite frequently - see the link above on dashboard webinars.
One more option is to use the InfoPath filler and Merge Forms import functionality which will allow you to merge multiple forms into one form. This requires manually specifying the forms and it's a bit of a pain.
I am guessing that Don is talking about above is related to the unique IDs for the rows in the list. And, yes, you will need to provide some way of marking them for the same employee but I'm guessing you are just using account ID or something unique like that. The real issue isn't the unique keying but rather how to aggregate the data.