I have got RNA-seq reads from Illumina which I've trimmed adapters using trimmomatic and then aligned it with reference genome using hisat2. Now I've run through string tie for transcript identification and quantification. I would like to use ballgown for differential gene expression determination. Please advise if the pipeline I 've followed so far is right. also, I would like to use Ballgown for differential gene expression determination. Can anyone advise me on a good documentation for ballgown usage?

Your apporach sounds good although a few details are lacking to really judge it. I would suggest you take a look at stringtie's homepage where they make a nice outline including links to Ballgown usage.