The choice of magnification level depends on which step of the fecal examination process you are in . When you first load a slide for viewing, you may choose 40x for a quick/partial scan, looking for major loads of larger parasites like fully formed Pinworms or Strongyloides etc. Then you might either drop into 100x or 400x depending what you are looking for. For example, if this is a follow-up check during weeks treatment for Coccidia then 100x will show them without spending 4x the time (400x vs. 100x) scanning the slide. If you suspect Giardia then you'll probably want to be scanning at 400x.
Bottom line is that if you have plenty of time on your hands then scan the entire slide at 400x and take photos of anything interesting .
P.S. 1000x is rarey useful for the kind of parasite hunting that we do with our microscopes.