I’m unsure when to check “Add HTML Cover Page.” I am compiling for an ePub that readers will download from BookFunnel. Later, I will be submitting this to Smaswords.
Unchecked, the iBooks and other readers have the cover (it shows in the library, for example), but you can’t page to the cover in the reader.
Should I check it?
These days, I think that option is mainly a matter of taste—whether you want a full-size image people can see in the reader view (what you get with Kindle by default). In the past, the presence of an image at the very beginning of the book would have been necessary for some programs to draw a thumbnail cover, as ePub did not start out with a formal cover page mechanic like Kindle did. So it may still be a good choice if compatibility with older reader software/hardware is a concern.