How do I stop a secondary display from switching away from fullscreen apps?

I've currently got a external display as a primary display, hooked up to my MBP running Mavericks.

Basically the problem is launching an app will disrupt a fullscreen app on another display. For example Chrome is fullscreen on the internal monitor and I launch System Preferences on the external. System preferences launches fine, but now the internal monitor has switched away from Chrome to another Space.

This is somewhat annoying because I am using the internal display to show lecture notes fullscreen in the background, while I am using different apps on the external. The only way to prevent this switching is either to not fullscreen the apps, or get rid of all spaces on the internal monitor so there is are Spaces to switch to.

This seems counterintuitive to me. Is there any way to launch an app without disrupting a fullscreen app on another display? Perhaps there is something wrong with my setup?

Any help would be appreciated!

edit: like so