However was the software for all the Amigas written as if as for a 32bit machine?
Unfortunately not. The worst example (in my opinion) is that in the old days some programmers treated it more like a 24bit computer (since the 68000 has 24bit addressing as chiark says), they would then use the upper 8 bits for storing other data to save a little memory. This kind of technique will generally fail on a 32bit system.
