A employee will work for two companies within a group of companies, I need to know what is the best practice in SF to be able to do this. She is currently hired with a position and a company had thought of creating another user but by standard it only allows one per person and instance
What are you referring to? Because nothing comes to mind when looking at the word collaborator (not a term that rings a bell for me in SF).
Generally speaking, it sounds like you could use the concurrent employment feature (that allows the user to have 2 users. hence 2 companies/positions that have 1 common person-id-external).