Hi,
It bit difficult but possible.
You can create two docker containers and limit each docker to a certain part of your project and then you open two instances of Cursor and connect each one to a container and there you have absolute isolation. it must be planned well otherwise you will be frustrated. you must plan if you need tight separation or a shared area in between.
if it is about frontend and backend, you might want to give access the other side of the fence for the LLM to read and make decisions. The new Cursor can manage this too. Read the release docks too, before you make up your mind.