Multi Window, when in it's original state directly from factory, doesn't allow you to use any app you want. You can only use a limited selection of apps. That's why developers felt the need to create something that will allow to use any app you want in Samsung's multi tasking mode.
How to enable all apps in Multi Window?
First of all, in order to make this work you will have to root your S4.
If you don't want to Do this, then I can't help you any further. If you are already rooted then let's continue. You have to two download XposedInstaller_2.1.4.apk
which will help you enable the mod.
After you download the files, install xposed 2.1.4 apk on your phone. Then install the multiwindow apk.
Enter the Xposed app on your device and click on install, then reboot. Then go in the xposed app and check the multi window module. Then perform a last reboot and that's it.
Now just drag the apps that you want in the Multi Window panel on the left and then drag any two apps on the screen to run them simultaneously.