I agree, publishers and agents don't expect to see the illustrations. The manuscript should only include the text. I believe that the easiest way to organize the manuscript is to indicate each page with the page number between parenthesis. Also indicate actions or expressions not specified in the text that need to be reflected in the illustrations between parenthesis. Example:

(1)

(ILLO: _____________________________)

(2)

I agree, publishers and agents don't expect to see the illustrations. The manuscript should only include the text. I believe that the easiest way to organize the manuscript is to indicate each page with the page number between parenthesis. Also indicate actions or expressions not specified in the text that need to be reflected in the illustrations between parenthesis.