1. Do the export as you normally would from your filemaker application, including the filename and format you want. (You will understand why in a moment)
2. Go into the Scriptmaker, double click on the script that you are using to do the export. This will bring up the script definition window. Then simply click okay, you will be presented with a window regarding saving or replacing certain actions (Find, Export, Import).
Export should be highlighted, select the "replace" radio button. Click okay.
This will now replace the preferences for your export with the ones you generated in step one. This works the same for finds, sorts etc. I assume that's what your after?