Unfortunately, this just is a significant workflow shortcoming of composing in Lilypond. For me, it is outweighed by the workflow benefits of Lilypond, the most important of which is that, since the files are all plain text, it enables me to use Git to manage my composition projects.
When starting a new project, I would suggest initially setting up every instrument with something like
R1*32
R1*32
R1*32
R1*32
rather than a single R1*x for the entire duration. The actual lengths are arbitrary since you will probably change them as you go, but the point is that by doing this, you give yourself a way to work on different sections of the piece before you've written everything in between. Any time you add music to an instrument, subtract from the rests however many measures you wrote. That way you will always have easy to find landmarks in the code for each instrument that sync up at the boundaries of the sections, as initially defined by the groups of rests.
It helps to always stick to one measure = one line of code, unless it would be excessively long, with a bar check at the end of every measure. \overrides and such should go on separate lines. Generally speaking the examples in the Lilypond documentation follow these practices and are a good model for style.
You're going to get very good at mental arithmetic adding and subtracting measures in large Lilypond scores, I'm afraid. (:
Saul