Note that you must have all your System16 ROMs zipped in various directories and all Raine related images in other directories in order to configure System16 as easy as possible.
1) First create an Emulator entry for System16 emulator:
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2) Go inside emulator in List View or over it in Tree View and press Alt-F10 (or just right click the mouse and select Emulator Manager). There fill Emulator (System16) properties. Note that if you have all zipped ROMs and images each in various directories on your disk, you can take advantage of "Emulator zipped ROMs paths" and "Emulator Images paths".
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3) Press "Update" button to update System16 settings.
4) Go inside emulator in List View or over it in Tree View and right click the mouse. Select "Add New Game". Fill the properties of the game and press OK to add it to the emulator. Note that System16 requires the games to be in a subdirectory called "Roms" under main System16 directory. So do not forget to fill "Emulator Specific Directory" as shown below!
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5) Repeat step 4 in order to add as many games as you wish.