Step one: identify material for the book.
I just sat and made a list of strips that I knew I could reprint - this was done in two simple columns, the left column was the title, the right was the number of pages - a little like this:
|Title||Page Count||The Tallyman#1||3||Broken Claw||6|
I basically included everything I thought I could get my hands on, excluding anything that would've been considered a second episode. At this stage I had something like 35 pages of material. Although I only needed 28. (You'll find comic page counts are multiples of four).
Step two: Identify what can fit and where.
The next step was to draw out a mock comic, a large A3 sheet with boxes drawn for every page. Then I got hold of some post it notes and wrote the comic strips out on them - each page of strip would get a single post it note. Then I was able to lay out on the mock comic exactly as I would like it.
Step three: Layout the comic in your dtp application of choice. I'm lucky, through work, to have access to adobe Indesign and was able to do a precise layout of the comic (including bleeds, etc). Which then allowed me to produce a PDF which was sent to the printers.
And that's it.