everything you add to your project will keep the same folder hierachy. So lets say you have a folder called myfolder and in there a file called myfile.dat. Then you would need to do:
fid = fopen(fullfile(ctfroot,'myfolder','myfile.dat'))
You can also compile once and not embed the CTF. After compilation, open the ctf file in some zip programm and take a look at the folder structure.