Generated two files, one for treatment and another for control using salmon. I have two quant.sf files. the tximport documentation/instructions seem very opaque, it is not clear how to import the specific files and carry out  the comparisons

You might need tximport and then (for example) DESeq for the differential analysis.

You shoud have a look at :

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

tximport is just for importing data, it does not contain statistical tests for comparing samples. You could use DESeq2 after tximport. Read the tximport vignette section on handing off the data to DESeq2, and then you can read the DESeq2 vignette for the rest.

Note that you don't have replicates, so you can't perform accurate differential expression. You should read the section in ?DESeq about experiments without replicates.