In most cases, with a handful of programs (SCCP, SCDP, VSD, WFB, and a few others I'm sure) they create specific files that contain your entire projects files. In all of these cases non of the programs have import ability so you cannot import changes made outside of the program.

Hence, your comment is 100% correct, always best to do all the changes you can inside the program and make sure it's complete and working as intended "before" editing anything outside of the program as it will not be imported and most likely will overwrite what you did.

You can however, alter the themes for the program to give yourself some base systems to work with so you don't have to go make some of the style and positioning changes outside the program. These articles with help with that:
http://www.coffeecup.com/help/articles/ … r-windows/
http://www.coffeecup.com/help/articles/ … er-themes/

Have fun with it and good luck!