I'm not sure of your chip's specs/capabilities so this may not work but take the 8052SBC for example. You can do ISP with it to program the internal flash or use the SBCMON and program the external memory (I'm not saying steal his code but just learn from the concept). This does require more than one computer program but it does appear to do what you are wanting (ofcourse I could be misreading what you are really wanting). Ofcouse you would need to add switchs/jumper/whatever to select which mode of operation you wanted but I don't believe that to be too hard.

Oh well that's just my thoughts, there is a lot of good information to spark ideas from just in that sbc (wish I could afford one :P )