We were in Poland around the same time of year (mid to end of September) a few years ago. The weather was very nice the whole time, and I didn't notice a big difference in temperatures between the north and the south.
We flew into Warsaw and spent a couple of days there, then went up to Gdansk and made our way back down to Krakow. It worked very well that way, but I can't say that it would have been any different if we would have gone the other direction.
When you are in Krakow, be sure to take a side trip to Zakopane. It's a beautiful mountain town.
I hope you enjoy Poland as much as we did. We will actually be going back this October and can't wait!