Setting default "Spaces" arrangement in El Capitan
The whole thing is much easier to manage if you don't use the system full-screen, which will always set a full-screen app to the right of any existing Spaces &amp; they cannot then be accessed by the standard  Ctrl ⌃   num  method

If you don't full-screen, then you can quickly lock any app to a Space by right-clicking in the Dock.

Also, make sure you don't have it set to rearrange Spaces automatically in System Prefs > Mission Control.

See my answer at https://apple.stackexchange.com/a/179403/85275 for some more working methods.