When you start either program for the first time it will create a library. So that's where they both came from. But maybe you only need one.
Open them each. (And check its file size too.) If one is totally empty, trash it. Then make sure each program opens the library that remains instead of creating a new blank one.
To force-select a library hold the Option key while opening the program. It will ask which library you want to open. The program will remember that forever until you change it again.
(If you find that you have photos in both libraries, use Aperture to merge them. Open one and then import the other one. I'm not positive but I believe it will COPY them over an you can then erase the old library once you've confirmed that copying worked.)
EDIT: I found this
http://support.apple.com/kb/VI159