I have a report Transformation based on the GST return can I save this back to my folder with the other import files
Dont worry figured that out as well
Submission back to to download page was also possible in the past however it appears that process has changed.
Personally I think some change is a good idea as submissions to the generally available localization page should have at least a basic human QA review first in my opinion.
I did it I opened the original in notepad++ and did the changes and saved it as a .json file and away I went oh I renamed file in code. so I have finished the import gst including the table works with no import gst and just 15% gst and works with just import GST and no other GST. so I think I have done well 
Purchase adjustments are a different matter because that involves manual input and that is beyond me scope