This must be a printer or rather firmware related issue....I use Repetier firmware and have a dual extruder printer. While support for using two extruders is limited for now in Astroprint I have had no issue either selecting the second extruder from my printer controls or by placing the T1, T0 commands into the start codes....For me AstroPrint seems to just assume what ever the current extruder that is selected is the one it will use....
My understanding might be flawed but I think the AstroBox just relays G-code to the printer...The only thing it seems to add is the code set in the Cancel Code in the printer setup on the astrobox itself if the print is canceled.
When it comes to Slicing start and end code are used by the cloud slicer based on the method of the individual slicer which are slightly different Cura vs Slic3r....adding the T commands an most other seems to work as expected.
I was a bit put off too when it seemed that AstroPrint could not deal with dual extruders but what I have found is that the Interface is weak when directly controlling the dual extrusion printer the slicers support it pretty much the way the do as stand alone apps, and when on occasion the cloud interface is limiting using the stand alone version of the slicer and uploading to astrobox seems to work okay.
Here is hope for full support in AstroPrint of all slicer and printer features like dual extrusion, bed placement, fan control, and all the others that the Astrprint guys are working on and Thanks for all the benefits we users already to enjoy for next to no cost.