Put the bottom left corner at 0,0 and the top right at the size you need to make the map fit such as 250,250. Once you've done that when you save as a png just make the map either 2500x2500 and you'll have 100 pixel grid... just also make sure when you save as you enter the values of 0,0 and 250,250 when selecting the map corners.
ONce you get used to that it should be quite easy to figure out what you need to do.

