OK, so i spent the entire day re-working my former theory. Rather than importing all the files i needed through the visual studio GUI, i copied everything from the original location on my c drive to the Resources folder automatically generated by VS in my new project add-in folder. Similarly, rather than put it in the Resources folder, I could have also used a new folder e.g. "data".
By adding these data files to the add-in folder, I can access any of the files statically. In my addin users can click on/off provided layers from a dockable window, similar to the TOC. If a user switches one on and it doesnt exist, it will add the file to the current view and the TOC. This involved .gdb, shapefiles and layers.
NB: Make sure that all you file sources point to the Resources (or new) folder where you are adding it from. I found that .gdb because windows stored it as a folder with files, i could certainly not go through the VS GUI, but add it manually. Dont worry if it doesnt show as openable.
I then add my layers etc programatically, getting the path name from the assembly directory.
Any more succinct thoughts on all of this/alternatives would be good.
Thank You
Alex