1. The percentages refer to mileage earning. You earn X% of mileage flown for a given class.
2. Yes. You must travel in a class that earns miles. Then you will earn full amount of XP. But Air Europa sells a lot of non-earning classes including discount business class, which earn 0 miles and 0 XP.
3. Don't create accounts in Air Europa. Access your booking through reservation code only. Then you can add your FFP number. Alternatively do it on check-in.