That last point is maybe something that needs to be called out. Make mistakes. Try things. It doesn't cost you anything but time, so get a basic set of compile options in place, run the compilation, look at the resulting pdf, and then go back and tweak the options as necessary. I'm going to guess that it took me about a dozen attempts to get what I wanted on the screen, but even then, I should have gone one step further, because...
Print is your friend.
Considering the ultimate goal is to end up with a printed book, I don't know why I didn't print some sample pages and make my own little "test book" to check font size and margins and such. I should have. Instead, I had to see that first proof copy from CreateSpace to realize that my margins and font size were wrong. I should have printed some pages at the 6x9" target size, cut out them out and taped them together before ordering that proof (which I did do before the second round of prints!).
Even then, I would not have known that the gutter margin was too small. I didn't even realize it when I paged through that first proof copy when it first arrived. Which leads me to my final suggestion for interior formatting...
Read the book!
Honestly, it took actually reading the book to realize that the gutter margin (the one closest the spine) was too tight (increasing from the original 0.75" to 0.825" for a 228 page book). By the fourth or fifth time I had to pull the pages nearly flat, I had sussed the frustration that readers were going to feel. Added bonus? I caught a few mistakes in the text (added space before a period, "where" instead of "wear", for instance) that had slipped past proofreaders as I read the book as an actual book.
I'm not sure I'll need to do two rounds of proofs on the next book now that I have working margins and fonts in place, but you'd have to be exceeding lucky to get everything 100% right the first time around. Even now, there are nits that I have to pick with the finished product, but they're not show stoppers. Also, they're on CreateSpace's end and thus not something I have any power over.
Oh, and don't forget to kill your widows and orphans once you have margins, font, and font-size determined (if you're so inclined)!