The rake shown in PT3 is the amount of money (rake) taken from pots that you won - i.e. the rake that you paid personally.
Depending on the deal you have, your rakeback may or may not be based on that value. In fact it is unlikely to be based on that - most rakeback deals work on some kind of proportion of the rake based on the number of players or the proportion of the pot you contributed. There are a few different methods in use, and we have a few custom stats available for free download from the
Customize PokerTracker section, but if your deal uses a different method we'll be happy to help you build the relevant stat to calculate it.
You may also find the MGR stat useful - that shows you the amount of rake taken from a hand divided by the number of players dealt in.