You are finding that homes built to the family of the 1950's and 60's and in now way able to meet the needs and expectations of today's family.
Your best approach will likely be to find a total solution for the problem. Today's needs include a two bathroom scenario at the very least. With this said, the locations of such facilities should be a major consideration and you'll likely find (hopefully not too late) that having baths in the basement and second level will not get it done. Future buyers will see this as a huge inconvenience and render your home as likely flawed for the RE market.
With this said, in my opinion your absolute best choice is to "bite the bullet" and do what needs to be done to locate the bath where it should have been in the very beginning....on the first floor.
Good luck with your decision.