You can watch a video presenting this tip here.
By default, SideNotes opens Search window once you press ⌘F ‐ just like other apps (the app to be open and visible.)
However, you can define a global shortcut that is always available. No matter if you're using SideNotes right now or not, you can always start searching. It also works if you're working in any other app in full screen mode.
To define the global shortcut, go to Preferences → Shortcuts and find Search item in Global Shortcuts. Click on the box next to the label (it should be Record Shortcut) and press the key combination you like to use. We recommend ⌃⌥⌘F, but it's totally up to you.