First off, welcome to the Org, rockoutloud1213! Good to see you here

Quote Originally Posted by rockoutloud1213
I am playing France in the early period. I've played VI before but this is my first time playing the normal game. I have forced England off the European mainland and was surprised the Pope hadn't warned me yet. However, when I followed them back and took Wessex, I got a warning to "recall my troops" in two years.
If you have twice as many provinces as the Catholic faction you're at war with, the Pope will warn you to back off -- this applies even to large factions that are attacked by small ones. That's why the HRE get excommed so often, as even launching counterattacks to regain lost territory still counts as "offensive" action in the Pope's mind.

Quote Originally Posted by rockoutloud1213
Does this mean I just need to stop fighting England (fine with me, I need to focus on the Germans) or that I need to leave Wessex?
You'll also need to withdraw your troops from Wessex. Alternatively, you could assault London instead -- if you take the castle immediately, you can often avoid the excommunication (but not always!).

Quote Originally Posted by rockoutloud1213
Also, what happens if I try to ceasefire with England as the Pope requested, but William doesn't want to?

Thanks.
Then you'll remain in a state of war with the English until either they offer you a ceasefire, or you're able to finish them off at a later time. I know it sucks, but them's the breaks. On the other hand, the Pope can only warn you against one faction at a time, so you're now free to attack other Catholic factions with impunity (at least for the next 10 years, until the current Papal interdiction expires).