TIMESAT Quality Data

I am trying to analyse time-series images from MODIS (MOD13Q1) in TIMESAT to clear the noise and get an output.

With EVI images I got also QA. I have to use it because there is often a cloud cover in my working area. I saw a few answers how to weight a certain range of values but I am not sure about it, especially because there are only 3 rows in TIMESAT. Can you give me an example of how to weight a MODIS data?

After reading many manuals and articles I still feel uncertain about my work and I have a couple of questions.