By default Texpad, on both iOS and OS X, examines your LaTeX source and opens any subfiles that have been included using tags such as

    \include{x.tex}
    \input{y.tex}
    \usepackage{a}    % a.sty
    \usepackage{subdirectory/b}    % b.sty in directory 'subdirectory'

Not only are these subfiles opened automatically, they're listed in the Outline View for you to work with all your LaTeX code as a single project.

On iOS, these tags are even more crucial when working with Dropbox or using the cloud typesetter: files are detected for downloading from Dropbox and for dispatching to the cloud typesetters based on these tags.

If there are files that are not being recognised by default by Texpad, it is very likely to be due to their having a non-standard file extension. You may force Texpad to load such files using the following comment in your LaTeX source:

    %force-texpad-dependency: file.ext

Note that the full or the relative path of the file must be specified including the extension.