Steven,
That's where the custom designed spectroscopy software comes in....
Programs like ISIS or BASS Project will do all the stacking and alignment for you and provide a solid means of selecting and binning the target Spectral image as well as the necessary background sky removal.
I'd suggest running your data through one of these programs.
I use BASS Project for the processing of all my Spectral data.
Ken
https://uk.groups.yahoo.com/neo/groups/astrobodger/info
http://www.astrosurf.com/buil/isis/isis_en.htm