This was a few weeks ago now, so maybe you've solved it, but for posterity this was how I solved the same problem.
Once you've imported the project into Eclipse, you need to add the mopub-sdk\src\main\java folder as a source folder. You also need to make sure you have all the dependencies present in the MoPub libs folder. As of yesterday, the dependencies I needed were:
- mopub-volley-1.1.0.jar
- android-support-v4.jar
- android-support-v7-recyclerview.jar
The website lists the annonations jar as well, but then you end up with this. It's already part of later versions of the support-v4 jar.
I also had to change my compiler compliance level in Eclipse. At the moment MoPub needs Java 7 features enabled.
I felt a bit mislead by MoPub's "hey just download this and press this and it will all work" type of tutorial. That they don't mention dependencies or the other problems seems a bit of a con to me. Sure, most of the information is there on the website if you look in their full integration help, but their basic tutorial makes it seem like there are no dependencies and that their Eclipse project is all set up nicely. Not so.
Good luck!