This is based off a tutorial I made for Mupen64 Plus on an Android based handheld, but since I got a steam deck, I wanted to get it working in Retroarch as well.

NOTE: This tutorial uses Retroarch installed via EmuDeck.

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Step 1: Prepare the Games

First you need to change some in-game settings in both games. Specifically the control scheme and aspect ratios.

In Perfect Dark
Make your save file, then in the pause menu, scroll to Options > Video

• Set "Ratio" to 16:9.
• Turn on Hi-Res if you need to.
  (Back to Options) > Control
• Set Control Style to "2.4 (Two-Handed)"
• Reverse Pitch: [OFF]

In GoldenEye 007
(You actually need to start a mission and bring up the pause menu.)

• In the third tab, change control style to "2.4 Goodhead"
• In the next tab over, set Look Up/Down to "Upright"
• Further down in the same tab, change Ratio to 16:9

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Step 2: Switching to Widescreen

(This assumes you set 3D games to "4:3" from EmuDeck. I'm not sure what effect having that already set to "16:9" will have on this process. However, if it is a problem, you can probably just skip this section and go straight to the next one for controls.)

While in either game, hold the select button and press Y to bring up the in-game Retroarch menu.

Navigate to Settings > Video > Scaling.

• Change Aspect Ratio to 16:9, or 16:10 if you want to fill in a little more screen and don't mind a little vertical stretching.

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Step 3: Remap the Controls

(Don't worry about these changes. We will save them to their own profile so they won't mess with other games.)

Go to Settings > Input > RetroPad Binds > Port 2 Controls.

• Change the Device Index to "Steam Virtual Gamepad" (Or otherwise the same controller as Port 1).

Navigate to Quick Menu > Controls > Port 1 Controls

• Disable the R2 button by switching it to "---".
• Disable all four Left Analog functions as well.
• Remap all Right Analog functions from "C Button" mappings to their equivalent "Control Stick" mappings. (For example, change "Right Analog Y- (Up), Axis -3" from "C Buttons Y -" to "Control Stick Y -", then do the same for the rest.)

Exit and switch to Port 2 Controls

• Disable L2 Button
• Change R2 Button to "Z Trigger"
• Disable all Right Analog functions.

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Step 4: Save Your Settings

Exit Port 1 Controls and go into Manage Remap Files

• Select "Save Remap File As" and give it a name you'll recognize. (This is to make setting up the controls in the other game faster. I chose the name "goldendark".)
• Next, select "Save Game Remap File".

Navigate back to Quick Menu > Overrides

• Select "Save Game Overrides"

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Step 5: Setup the other game using your saved configurations.

Launch the other game & open up the Retroarch quick menu.

Navigate to Quick Menu > Controls > Manage Remap Files

• Select "Load Remap File" and choose the one you created. (goldendark.rmp for me.)
• Select "Save Game Remap File".

Navigate to Settings > Video > Scaling

• Change "Aspect Ratio" to 16:9 (or 16:10).

Navigate back to Quick Menu > Overrides

• Select "Save Game Overrides"

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There you have it. Be sure to get retroachievements up and going as well, and have fun in your espionage shenanigans.