You should always put the schools on your CAF in the actual order that you prefer them.
There is a post here about the equal preference system: viewtopic.php?f=5&t=28840
It shows that the school puts all the children who name it anywhere on their CAF in a ranking order according to the school's published admissions criteria. It doesn't make any difference to your daughter's rank whether you put the school first or last on your CAF. But if you do put it lower down on your CAF and you're offered a place at a school higher up, you will never get an offer from your actually preferred school.
The schools don't know where on the CAF you have put their school. The letters from the school are just to remind you that if you want to go to the school, you should name it first.