There really isn't a way to save the game manually. I'm currently at 49%, but I've spent a lot of time doing side missions and exploring. During certain missions, you need to complete the mission to trigger the auto save feature to save your game. However during later missions you can save your game by climbing a viewpoint and synchronizing the view. After the video sequence is over, the auto save feature is triggered and your game will be saved. Also while roaming the homestead or frontier as Connor, you can kill an animal and then skin the animal to trigger auto save. I searched and tried to save the game manually and this is the best way save your game in the middle of a mission and not lose all of your progress. However, like I said, there are certain missions you have to play all the way through in order to save your progress. The early missions are a pain and I feel for you.