I have a 2 leg flight domestic. I have an option to upgrade only the 2nd leg when I check in online. If I pay the $50 for the 2nd leg upgrade, will I get 2 free checked bags for the entire trip?

The major reason for doing the upgrade is for the free baggage, so if it wouldn't get me through both legs, I don't want to spend the money. I'm really hoping someone can give me an answer fast because I fly today.