Can a program be set to use a different file manager?

For example when opening a file from a program some will open one file manager and some will open another one that does not have any of my file bookmarks. Than neither program will open a file manager that shows the bookmarks I set when using standalone caja. Is there a way way to make all programs use the same one? Or is this a setting that would be adjusted in each program individually? Currently running Ubuntu 16.04 Mate but I have experienced this on several DE