It is good you are reading and trying to understand what is going on before you jump into it. I kind of wish I had done that when I started
Yes you do boil off a bit of water in the boil. Just something you will need to learn about your system and take into account when you are warming up your strike water and mash water. Everyone is a little bit different but if it helps last night in a hour boil I was just short of two gallons boiled off.