I had problems compiling with the \includeonly \include system since I had images in the document form different subdirectories. For example the main file would be at /Main/MainFile.tex and the included file at /Main/Chapter1/Chapter1.tex and one of the images would be at /Main/Chapter1/Images/Image1.jpg which was actually loaded through the Chapter1 file as \includegraphics{./Images/Image1}.
I had the problem fixed with the import package using \subimport{}{}, but I don't have the include functionality of different .aux files which keeps the pagination and cross references intact.
How do I get the best of both?