If you've had the excom warning it's too late to imporve relations - you must back down. The relations apply when the pope warns you: If they're good your standing will fall if you fight on. If they were bad you'll get excommed. So you need good relations *before* you attack the other faction.
P.s. I'd just like to echo the others who say make an alliance with the pope. I was too slow in my first game with France (VH/Vh) and they allied with HRE (go figure). Although I could still bribe to get pope-o-meter up, call crusades etc I could not make him break the alliance and could not get the HRE excommed. No matter what I did they always stayed high and my rating fell wihtout constant cash, because I was at war with his ally. Very expensive.
In this game as scotland I allied and am paying a miserly 200 florins a turn. I'm at rating 7-8 and the English have been excluded from the grace of god!
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