Mine is set up this way. You can take a look here!
Even though my comic doesn't squeeze an entire chapter into a single episode, you'll see it's definitely the same format. I make a thumbnail for the entire episode in one canvas, in low resolution; then I crop it into pieces, make them bigger and work on them as separate files. Once all of those pieces are complete, I put them together into one huge, long high res file.
THEN I shrink it for web viewing, and cut them into pieces again. XD That sounds redundant, but it's necessary because sometimes the pieces overlap (like if there's a continuous gradient connecting the pieces in the gutter). I have to put the pieces together in high res and work on the overlapping parts so I'll have a high res version of all the work -- including the overlapping parts.