Step 1. Rip your CUE file from your OWN disks
Step 2. Put your CUE files in the same folder and go to Notepad
Step 3. Copy the names of your CUE files and put them on their OWN LINE
Step 4. Press file-Save as…
Step 5. Press .txt and change to all files
Step 6. Put as an M3U file in the SAME FOLDER AS YOUR CUE FILES
Step 7. Play the M3U file in RetroArch
Step 8. When it tells you to switch disks, open the quick menu
Step 9. Go down to Disc Control
Step 10. Press Disc Cycle Tray Status
Step 11. Resume game
Step 12. Re-open the quick menu and go back to Disc Control
Step 13. Change the Disc Index to 2
Step 14. Resume game and press start
Now the game should load disc 2 and you can continue playing.