Planning for an adventure

Been a while since I posted.  One thing I find is that preparing for running an adventure is something that gets easier when you do it all the time.  I'm finding I'm really a bit out of practice as I prepare to run the first adventure of the Freeport trilogy at an upcoming August weekend.  Here it is June and I'm really enthusiastic about this but it feels like it's a slow process.  Of course, some of that is probably the character creation process which a) normally wouldn't be the case if the players were making their own characters but this is essentially a one shot so I'm doing pre-gens and b) involves the Pathfinder system which is close to 3.5 but different enough that it's a learning curve.  But while I've read the module a number of times I still have a lot to do converting/learning the encounters and planning the visual presentation of the encounters with maps/tiles and minis.  I'm still confidant I can do it by August since it's not even July yet but I'm trying to recall if it's felt like this before.  What steps do you go through when you normally prep to run an adventure from a published product?

Storage and presentation

I recently added a five shelf bookshelf to my game area to make more of my game books and materials accessible.  In arranging stuff, I was wondering how most people like to store their RPG books.  I usually try to group like game materials together and make the most likely to be used the easiest to get at.  But do some people put stuff on the shelf chonilogically, alphabetically, thematically?