With the news that the PB tool is going to be free I've begun playing more with larger books. Last night I learned some lessons while converting CCEL's Summa Theologica to PB.
1) When dealing with Large Word Documents let the resource repagenate completely before starting to work with it.
2) Give everything a style and minimize the number of styles used. It's a lot easier to simply modify a style then to go line-by-line through the document.
3) Don't double space. This resulted in way too much space between paragraphs when I brought it into Logos. Instead Single space everything and apply different paragraph spacings to your various styles.
So far I've worked on two larger resources, both from CCEL; Summa Theologica-Thomas Aquinas and Exposition of Scripture: 2 Cor, Gal, Phil, Col, Thess, 1 Tim.-MacLaren. Below is a screen shot of what they look like in L4. I highly doubt Summa is at the Logos version's quality. There are many errors in it and I do not know how many of them are a result of my formatting procedures and which are inherent in the CCEL version.

What PBs are you working on?