I currently have several paired-end RNA-seq datasets scaled to rpm in bedgraph format (thanks to a former biostar question post reply that was very helpful! :)).

Is it possible to work from these files as they are, and split them into two tracks, one with only positive strand reads and one with only negative strand reads? Or is it necessary to return to the original bam files to do this? Either way, how might the command lines look, and how will the fact that these are paired-end datasets influence the commands I have to use?