When you upgrade MacOS X by installing the update on top of the current system, all your documents and data and applications will stay just a they are. Some applications may no longer be compatible or plug-ins they are using may not be compatible.
Incompatible applications will have icons that are crossed out like the ghostbusters sign and you will have to update them. RoaringApps is a good place to check older apps for compatibility before you take the jump.
Don't upgrade without making a full Time Machine backup or a bootable clone of your Mac. This way you will be able to revert to the current state, if something should happen. This document describes how to revert back to the previous system from our backup: OS X Yosemite: Revert to a previous OS X version
Have you checked the "App Store > Purchases" tab, if iPhoto is showing in your Purchase history (the fourth tab of the App Store)? If iPhoto is not showing there, when you sign into the App Store with your Apple ID, you will not be able to update to iPhoto 9.6.1 without the Help of the App Store Support. Check that before you upgrade to Yosemite. Your current iPhoto version is incompatible. If you cannot update from the AppStore to iPhoto 9.6.1, you will need to use the Photos.app instead of iPhoto.