If you are following the templated Transcriptome/RNA-seq workflow, an additional checkbox appears in the Input Sequence Files and Define Experiments or Individual Replicates dialog: Stranded RNA-seq data. The box is unchecked by default.
As background, some library preparation methods preserve the directionality of reads, i.e., reverse reads always point 5’ to 3’ in the direction of transcription, while forward reads point from 3’ to 5. If you want SeqMan NGen to determine whether reads come from the top or bottom strand of the genome, check the Stranded RNA-seq data box. Strandedness information is used in two ways: 1) to disambiguate transcription from overlapping genes on opposite strands, 2) to allow the SeqMan NGen assembler to properly allocate reads from overlapping genes. If you check the box, launch SeqMan Pro after assembly to view the results in the form of color-coded reads.