Coming from CrossOver, Whisky, Not Proton or Game Porting Toolkit

Superposer looks for what other tools left on your Mac and lists it on Setup (Coming from another tool) and on the Steam Integration page (Bring your games over):

CrossOver bottles (~/Library/Application Support/CrossOver/Bottles), including a bottle with the Windows version of Steam inside;
Whisky bottles, wherever Whisky keeps them;
Wine or Game Porting Toolkit prefixes in your home folder (such as ~/my-game-prefix) or in ~/Games;
Not Proton, and what it changed in Steam.

Superposer only reads other tools' bottles. Nothing in them changes, and you can keep using that tool.

Bringing a Steam game over

For each game found in a Windows Steam inside a bottle, Bring Over… shows what can come along, and nothing changes until you choose Bring Over:

Settings. The bottle's graphics choice (D3DMetal, DXMT, DXVK or WineD3D), MSync, High Resolution, Metal HUD, Advertise AVX and DLSS → MetalFX become the game's own settings in Superposer (Per-game settings). Settings without an equivalent are listed, not copied.
Saves. Folders in the bottle's Windows profile that are named like the game (in AppData, Saved Games or Documents › My Games) are ticked; others found there are listed so you can add them. They're copied into the game's own Windows folder on this Mac. Games with Steam Cloud get their saves from Steam anyway.
Game files. If the game is fully downloaded in the bottle, Superposer copies it into Steam's library on this Mac, so Steam shows it as installed and doesn't download it again (only an update, if one came out since). On the same disk the copy is an APFS clone: it takes no extra space. Move them out of the bottle is there too, but only when you choose it; the other tool then no longer has the game.

Quit Steam first: Steam's library changes. Steam integration must be on.

Superposer doesn't point Steam on your Mac at the bottle's own library folder: Steam would then write into the bottle (downloads, updates), and the bottle would no longer be the other tool's.

A game that has a Mac version on Steam is left out: Steam installs the Mac version, which doesn't use Windows settings or saves. If it uses Steam Cloud, your saves come with it; otherwise the sheet shows where the Windows saves are.

Everything is recorded in Changes to your Mac. Removing the game in Superposer undoes it; the bottle keeps everything it had.

Coming from Not Proton

Not Proton changes Steam.app itself (it loads its own code into Steam and re-signs the app), gives Windows-only games its own tool as soon as you buy them, and can block Steam's updates. Superposer changes only Steam's settings files. Both at once is untested by either project, so the Steam Integration page says what Not Proton changed.

Switch Its Games to Superposer… sets the games that use Not Proton's tool to Superposer's (Steam must be closed). Superposer never changes another tool's setting without asking.
Not Proton's own changes are removed by Not Proton: open it and choose Remove Everything, which puts Valve's Steam.app back. Superposer never deletes Not Proton's files.
Your games keep their Windows folders and saves: Not Proton and Superposer use the same folders in Steam's library. Superposer updates a folder to its own Windows runtime the first time the game starts.
Launch options Not Proton wrote (such as CX_GRAPHICS_BACKEND=DXMT or NOTPROTON_RETINA=1) keep working (Steam launch options).

From Terminal: superposer import lists what was found, superposer import game <appid> shows the plan for one game (add --apply to do it), and superposer import notproton explains Not Proton's changes.