Reading how you wish to have your code segmented into structured files and organised in a way you want in the IDE is exactly how I have that same need.
Knowing how I program programs that I know will grow and contain various functionalities, such as the project you and I are both endevouring to do, I found the Arduino IDE was going to be a clunky way and most probably a very frustrating way for me to develop my project.
So, for me, spending some hours thinking about how best to do this, is exactly why I did move to using Eclipse IDE with the ARV pluging from Jantje.
I can have any project file open in any tab I wish.
I have something like 11 local files, which includes their header files, the main file with its header file, some imported library files together with Arduino library files.
So, you can see how, after a short while, the number of files grows, and with using Eclipse, I find it so much easier.
The workflow is a whole lot smoother, being able to pull up the files I am currently working on, while having others not open in a tab.
While editing, I do get to see quickly any sytax erros as I go, it prebuilds on the fly, not compile
I haven't worked with the Arduino IDE with multiple files but from what you have just mentioned, to me, it sounds horrendous to use if you can not organise your tabs in some way.
Yes, I needed a little while to throw myself into the understanding and becoming familar with this wonderful development IDE.
I guess what I am saying is that I find Eclipse with the AVR pluging totally awesome.
Below is a screen capture to help you visualise how I have it, click on the image once it is loaded to view it completely.https://plus.google.com/photos/101798763285299013446/albums/5803380788356187681