I used to modify the default file that came with the tg download, but now I make a new file with my desired settings and save it to a folder, like myDefault. Then, in TG, go to Edit|Preferences and choose Startup|Project Creation|Load from file and pick the new default file.
[edit] I should add, there's some nice options in the preferences -- give it a look. Since I added a SSD, I wanted to avoid using it so use the File Saving automatic render output choose location option to direct it to a different drive.