When diagnosing parasites, size does matter. The intestinal worm eggs are substantially larger than the protozoa, and so they can be frequently found and identified using a 400x magnification. When doing microscopic exams on O&Ps, it is always helpful to have an ocular micrometer to help with a definitive diagnosis.
As far as distinguishing one from another, this handy little chart helps differentiate species that might have a similar shape, but the differential characteristic could be the size. Sizes are shown in micrometers (µm).