Yes, don't worry, the rest of your teaching years on that school will be counted as well.
How can I know if I qualify as a highly qualified teacher?
You must meet some basic requirements to qualify as a highly qualified teacher, with additional requirements depending of if you are a elementary or secondary school teacher and whether you're new to the teaching profession.
And how do I know if I'm teaching at a low-income school? I worked in an Indian reservation school.