Hey theperv!
For updating to a new version, all you have to do is download either the high-res or compressed .rpa file, and place it in your "game" folder. I'd recommend deleting the old .rpa after doing this.
Saves carry over automatically so you can just boot up and play :)
(However if you ever want to backup your saves, you can find them in "ahitr_storage" and I'd also suggest backing up your persistent file too if you ever make backups!).
Hope this helps o/