We are adding 2 or 3 new subsidiaries with the same benefit plans as parent but different eligibility requirements. How do I set this up? Do I need to have seperate plan docs for each company, or can I just amend for the new subsidiaries?

You should only have to have one plan, but the participating related employers, parent and subsisdiaries, have different elgiblity requirements. You should line out the differences in a what we call a participating employer agreement and as well as in the SPD.