If it has vector-like drawing tools, you can still draw straight lines, rectangles and circles as usual. Just make sure that anti-aliasing is turned off and you use a 1-pixel hard brush. If it has objects or layers, make sure you draw each distinct element in a separate layer. If you muck it up, you can adjust that layer or delete it and start again without affecting the other layers.
If you have a transparent background and zoom in 800%, then each square of the checkerboard background corresponds to 1 pixel (at least in all programs I've used). This avoids needing a grid.