I have 8 BAM files from an RNAseq experiment (4 different individuals, 2 different tissue types per). The Illumina run was singled-end 50s and we have about 3.2million reads per sample.

I need to know how many counts align to the different parts of the reference genome from each sample identified by tissue type. I am trying to prep my RNAseq data to run bioconductor's DESeq2 protocol but I am stuck getting the count matrix to even start.

I have basically no programming experience; any and all help is welcome and explanations like you are talking to a child would be greatly appreciated.

Are you at a location that has a bioinformatics facility? You might want to get some help with the bioinformatics. 

Otherwise, read tutorials, e.g. 

https://combine-lab.github.io/salmon/getting_started/

https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html