You can't alter the permissions of the windows files (in a permanent way). The permissions you set on the windows files will only apply suring the current mount, when you return to windows, the permissions will be the same as windows ahd left them previously, and when you go back to linux, all your changes will have been lost to the permissions.
Linux doesn't control the windows permissions, windows does. The only thing important with a win file is that it can be read. Unless you have done something with the ownership on the files, you can't write to them (assuming you have one of the NTFS writing tools to write with).
If you could write to the directory containing the files, you should be aboe to write the files, unless there is ownership involved. Do ls -al (target) and see who owns the files. As root mounted them, probably root ownes them. You could change the ownership (again recursively) to give your base user more write permissions, but again, linux can't effect the true permissions of windows files.