Yes they will only be overwritten if you choose to update all the files. In most cases, you won’t need to do that if you’ve made a lot of customizations to your theme. Most updates are minor, and usually deal with small tweaks here and there. If you want to make customizations that won’t get affected by updates, then you could create a custom folder and import your custom files there. Here is an example – http://bit.ly/1rBUNAW