For cross era play am I subtracting the season rating from the team from that season or from their opponent from a different season?
You will add or subtract to the OFF rating based upon each team's SEASON rating.
The last page of the rules explains this in detail.
But, to be clear for your question here, you will use the Season rating of each team to adjust their OFF rating. So, if say you are playing State Tech and their season rating is -1, you will ADD one to their OFF rating for cross-era play. Let's say their opponent is Wild Card U, and they have a season rating of 4. You will SUBTRACT 4 from thier OFF rating. The Defense, SOS and HM ratings remain as they are on the rating sheet.