How to use the flatten transparency function

Been using Illustrator for years but this is the first time I've worked on a book cover. PDF looks strange when viewed in apple's Preview App. But looks fine in adobe acrobat. All my research concludes that this is because Preview doesn't read transparency well. Should I flatten transparency on my PDF, so there's no chance of a printing error, and if so, how? When I apply flatten transparency to the whole project, things get strange and objects disappear completely. Would love any help possible, thanks so much!