The one almost always consistent order is time: records are usually arranged in chronological order. I say usually because I have been frustrated by out-of-order records once, in a parish register book that was from the late 1500's to the mid 1650's. I think it was probably due to the pages themselves getting rearranged at a later date. Perhaps they were not secured in the binding and the individual loose leaf pages were just shoved back haphazardly into the book, placed on the shelf, and forgotten. The archives digitizes the books in the order they are currently in. That means there can be entire sections of books out of order!
I found something tonight that I had never seen before. I was looking for the "S" name of Štefek. Some variations of spelling for this name are: Shteffek, Shtefek, Štefek, Šteffek.
I found the "S" section of the register in question. I did not find any Šteffeks at all. I decided to check some other towns, to no avail. I scratched my head; the margin note in the wife's death record specifically said she died in Kunčice pod Ondřejníkem, and since she was also born there, it seemed the most likely place for her to have lived with her husband (who was a Trojanovice native).
After searching Trojanovice and neighboring Frenštát records, I decided to double check the Kunčice pod Ondřejníkem index. This second look rewarded my efforts with the answer: S and Š were indexed separately. I was able to use the separate Š index to find the records I was looking for.
I noticed they were indexed separately because I saw part of the next page peeking out while I was on the S page. I was confused at why there would be two "S" pages, when clearly this one was not all the way full.
I think that as the parish registers moved away from Latin and German and became more "Czechified" (i.e. closer to 1900's), it is more likely to see letters with diacritical marks indexed separately. For example, C and Č or R and Ř. Fortunately, there aren't a ton of these. But, it is a helpful reminder to non-native Czech speakers: remember that sometimes Czech names might be indexed separately if they begin with a letter with a háček!