When writing papers in latex, I usually use WinEdt and MikTeX (more recently, I started using SublimeText with TexLive), but most of my co-authors only use ScientificWorkplace with the dated TrueTeX latex engine.

In preparing papers, I like to have the following folder structure:

bibfiles/
project-files/
    |
    |-plots/
    |-tables/

But this does not work for SWP because in order to compile the main document, it copies the tex file to a temporary file under a temporary folder, and therefore, SWP cannot find any folders or graphics included with \input or \includegraphics that are in the above subfolders. SWP also cannot find any bib files, unless the bibfiles folder is appropriately selected in the general settings, or the bib file is copied to the standard folder: c:\SWP folder\TCITeX\TeX\BibTeX\bib\.

The solution, which does not require to manually edit any settings file under SWP (which does not work anyway), involves three steps:

1. To fix the issue with finding graphics files (e.g, png or pdf files, because I use pdflatex), include the following commands in the preamble. Notice the two sets of braces and the trailing /. The path can be absolute or relative (see 2).

   \usepackage{graphicx}
   \graphicspath{ {/path/to/graphics/folder/} }
   

2. To be able to work with relative paths and subfolders we have to prevent SWP from copying the main tex file to a temporary folder when compiling. This is achieved by setting the main tex files as a master document. Include the following code somewhere after \begin{document}:

   %TCIMACRO{\QSubDoc{Include subdoc}{\input{tables/subdoc.tex}}}%
   %BeginExpansion
   \input{tables/subdoc.tex}
   %EndExpansion
   

   The file subdoc.tex located in the tables/ folder has to include the following code (and it can be empty otherwise; it can also be located in the main folder, but the paths above have to reflect this):

   %TCIDATA{LaTeXparent=0,0,main.tex}
   

   where main.tex is the name of the master file. For additional files in the plots and tables subfolders, the TCI macro is not needed, and the usual \input or \includegraphics commands will work and the tex or graphics files will be found.

3. As mentioned before, to find the correct bib files, the options are to change the standard path in SWP's general settings or to copy the bib files to the standard path under the SWP installation folder, c:\SWP folder\TCITeX\TeX\BibTeX\bib\.

4. Finally, it goes without saying that your coauthors should always save project files in Portable LaTeX format.