Mode Z is the default. Select the mode by pressing the appropriate button (in short, the left shoulder button) on your pad on the Sega/title screen, or during cutscenes.
ABC act as normal, but default control scheme is changed to Left-All-Right, to support 8bitdo controllers.
You can also change the controls by pausing the game and holding up and then A/B/C/X/Y/Z. Pressing A/B/C will map the button that you press to all flippers, and pressing X/Y/Z will change the mode for the extra controls.
Left and right shoulders will always work correctly on the Saturn pad. THe analogue stick on the 3D pad is supported. Thanks to Sik for helping me sanity check my code.
Note for Mega SG users: If you are playing using a Saturn pad or using the Mode button, you need to enable passthrough mode in the system options. Saturn pads will not function at all without passthrough mode, and the Mode button will force 3 button mode if held down during gameplay.
Did you even know that there's an ongoing community effort to port the Game Gear library to the Master System? I like to help out by fixing up the controls. Do a ctrl-f for "Wafer" on this page to see, I'll make a proper list later, honest.
Surface navigation view to get a bearing for a given latitude and longitude in real time.
Neutron navigation view for following routes generated from spansh.co.uk/plotter. When you reach a waypoint, it copies the name of the next waypoint to the clipboard. You can also right-click system names to copy them to the clipboard. It also estimates fuel use.
Fleet view which lets you find your ships easily. You can right-click to copy the location to clipboard, click on the ship name to view the ship in EDSM, and click anywhere else to view the location system on the web.
Chat view that outputs message, timestamp, sender and the channel used. Supports copying to the clipboard (use Ctrl-X - NOT Ctrl-C). Outputs the system name when you start a hyperspace jump, with a link to view the system on the web and a right-click menu to copy to the clipboard. "Freeze" button to stop the chat from dropping to the bottom when a new message arrives, useful for if you're scrolling back whilst people are still talking.
Long Range Scanner view that allows you to query the stations in your currently targeted system. Great when looking for a place to refuel in the Bubble.
Materials Helper view that allows you to select engineering blueprints and simulate the costs. Clicking on the material categories at the top lets you simulate the relevant material trades. Caveat: no support for experimental effects yet.