Letters of recommendations and low GPA

I am a recent graduate from the college and am planning to go for Master degree in the next fall (2016 fall). I graduated with sub 3.0 GPA. Since I didn’t perform not quite well in my major classes, I am having problem whom to ask for the recommendation letters.So, I decided to take a year off to work in a lab which research area I would like to go for grad school and also to find someone who will be willing to write recommendation for me. So, I started working in a lab. The professor is awesome and I enjoy the work. After two months, professor told me to consider applying to his lab for grad school and he will ask for GPA waiver for me. My question is if I am applying for his lab, can I still use him to write the recommendation letters? Do the potential advisers read the letters?