This is unlikely to be necessary. Keep working in Builder and insert code components within the Builder interface rather than attempting to edit the generated script. The code component will automatically insert the code at the right place (beginning of experiment, beginning of routine, every frame, etc) and allows you to keep tweaking the experiment using the GUI. Best of both worlds.
This is a feature rather than a bug. i.e. can you think of a better way that PsychoPy should search for your file? The alternative is to use a full absolute path to your file. You are still able to do this of course: PsychoPy doesn’t prevent you), but that creates potential for errors and makes your experiment non-portable.