This is my basic workflow for getting manga/comics on my jbc.
Download all your chapters or whatever into a single folder where each chapter is in a separate sub folder.
Zip it up and rename as a cbz or cbr.
Open up comicrack(google it) and export the cbz or cbr to an image folder. This will give you a folder with a crap load of jpegs but they will all be in order.
Use
http://www.rw-designer.com/picture-resize to resize the images to 1600x1200
Use JpegtoPdf(google it) to make the pdf. Set Specify page size to 8.5in W 11.25in H and check shrink and enlarge boxes.
This may not be the best way to get comics onto your jbc but it works for me and it fills the entire screen.
I break down my Manga into volumes of 10. So one pdf will be volumes 1-10, next would be 11-20 ect. Works well for me.