potentially, yes - and move the end stops..
For my rep clones I use flashforge's flashprint these days, just so much better for the dual nozzles than simplify3d - and I've yet to find any way of changing bed size on it.
I've looked as I'd quite like to use it for other printers as well.

You could do it using simplify3d, or cura or slic3r.

But not flashprint or makerware - that I know of.