Is it a mileage run? - other wise I can't understand why do SEA - EWR - SFO in one day. You can connect from SEA to SFO on AS and get CO mileage and EQM.

When checking in at SEA, you need to mention the SFO connection at EWR so they will be able to guarantee the connection. Since it's CO to CO, if it's over 60 minutes it should not be a problem and they should take care of you if you miss a connection in terms of reaccomodating on the next flight out.
Since EWR is your "home" airport they will probably not give you anything except a new flight ticket (no meal and/or accomodation).