When you add Math project to the in path of science project, all of math project's code is sent through the aspectj weaver and properly woven. The results of that weave are written to science project's output folder (not Math project's). So, if you were to look in science project's bin folder, you should see the woven classes there.
If you wanted to keep the in path files separate from the regular files, you can specify an inpath out folder. This folder should also be added to the class path as a binary folder. Also, this folder should be placed above the project dependency to Math project in the "Export and Order" tab of the Java build page for Science project.
Finally, if you run the main class from Science project, rather than from Math project, you will be executing the woven code.