Ok, all should be installed, but before you can actually use disk images, you need to edit the /etc/emulationstation/es_systems.cfg file.

The command is.

sudo nano /etc/emulationstation/es_systems.cfg



Change the apple2 section from this..

  <system>
    <name>apple2</name>
    <fullname>Apple II</fullname>
    <path>/home/pi/RetroPie/roms/apple2</path>
    <extension>.sh .SH</extension>
    <command>/opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ apple2 %ROM%</command>
    <platform>apple2</platform>
    <theme>apple2</theme>
    <directlaunch/>
  </system>


to this..

  <system>
    <name>apple2</name>
    <fullname>Apple II</fullname>
    <path>/home/pi/RetroPie/roms/apple2</path>
    <extension>.dsk .nib .po .DSK .NIB .PO .do .DO</extension>
    <command>/opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ apple2 %ROM%</command>
    <platform>apple2</platform>
    <theme>apple2</theme>
    <directlaunch/>
  </system>