.cci (instead of .3ds)Check View > Fullscreen to start applications in fullscreen.
Uncheck View > Single Window Mode to start applications in separate windows.
Access the general settings by selecting Emulation > Configure.
Remember to unpause the application (F4 by default) when focusing it again.
The following are settings accessed by going to Emulation > Configure > Controls in the main menu.
Clear the F5 and F6 hotkeys for stopping and restarting emulation, respectively (they don't ask for confirmation).