Ben,
Tell us exactly what you do when you crop and we might be able to explain using your own example. But broadly you want to leave the third box from the left completely empty.
By all means put sizes into the height & width boxes if you want to, but never put a figure into the resolution box because the image will be resampled and detail will be lost forever. As a general rule of thumb try always to limit any cropping to a bare minimum. Your images should always have dimensions in pixels measured in thousands never hundreds. If you see hundreds, then somethings gone wrong.
An A4 sheet measures about 8.25 x 11.7 inches, if you print at 200ppi, then even allowing a half inch border all round, the image should be 1450 x 2140 pixels and the 5D and 40D are well capable of those minimum requirements. Personally, like others here have already said, I print mine at whatever resolution it ends up at, if thats 458.75ppi or 684.2ppi, then so be it!
