Hey Lace.
Here's the long and short of how the data in CaveStory is rearranged by CE. The beginning of the exe tells you how many sections of data there are and vague info on what they are. As I recall there's a .rdata, .data, .swmap (if edited in SW) or a .csmap (if edited in CE) and a .rsrc. They basically translate to read only data, code, editor added map data, and resources (all the ORGs, sound effects, etc.).
What both CE and SW do to rearrange the data is pretty simple. For CE I find the map data (in either the original location, SW's location or CE's location). Going from the original, I basically copy all the map info and create a new section called .csmap. I then save the data back to the exe in the same order I got it out, placing the .csmap section in between the .data and .rsrc sections. That way, the resource data is still at the end of the file like most resource hacking software is expecting. The only trick is there are a bunch of pointers at the beginning of the exe telling where all the sections begin/end so I have to make sure I update those to where all the resources are now that I shifted them further down in the file. Also, there are several places in the code that look at the map data so I need to adjust the place they start looking from too.
I hope that explains everything without being too dumbed down or too complicated.