I have diseased and normal samples. How will DGE analysis tools DESeq2 and Ballgown know that they have to analyse differentially expressed genes from diseased samples comparing diseased with normal. Where I need to set in DESeq2 and Ballgown? Kindly provide suggestions for both DGE analysis tools.

Your help will be highly appreciated.

Please read the vignette, it covers the basics in great detail. https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html