Does it make any difference how the files are layed out?
Yes, but as CD players have become faster this is less of a problem. The fastest access is for data on the inside tracks which is at the start of the CD. This is because it takes longer to seek data from the outer, or end, of the CD. Therefore, if your CD is written in disc at once mode, the indexing information should be copied to the CD before other data files. For a multimedia type disk, the location of files can be more important so files that are likely to be accessed together should be placed close to one another on the disk.
