When creating apps for both Windows 8.1 and Windows Phone 8.1, you typically want roaming data–as managed through the WinRT APIs–to work seamlessly across both.
Note that it's not necessary to implement the app with a universal app project in Visual Studio. Those project structures are simply a way to simplify development processes, and isn't a requirement for providing the same app experience on both Windows and Windows Phone.
The second requirement, however, is that both apps–however you build them–must have the same identify in their respective stores, which means specifically the package family name. This is what's used to manage the roaming settings, and so long as those match, then both implementations will work with the same roaming data. This is again a given with a universal app project, but something you have to do manually if implementing the apps with separate (non-universal) projects.
A little guidance on this can be found here: http://msdn.microsoft.com/en-us/library/windows/apps/xaml/dn630421.aspx
For some general Q&A on app data, which includes other aspects of roaming, see my post on the Building Apps for Windows blog: http://blogs.windows.com/buildingapps/2014/06/19/common-questions-and-answers-about-files-and-app-data-part-1-app-data/