The remaster seems to automatically separate save files between campaigns. To access your base game saves, just select "New ...

Once known as the System Shock 2: Enhanced Edition, this version features improved visuals, gameplay, and performance, as well as cross-play co-op multiplayer, mod support, and other features.

Nightdive explains once again why they made a System Shock 2 remaster instead of a full remake, now that it's finally releasing,.

System Shock 2: 25th Anniversary Remaster will additionally include upgrades to the game’s beloved co-op multiplayer mode and officially support fan-made content.