You reference the story in your cover letter as a rebus story. You underline the words that you visualize being replaced with pictures in the published story. In all other ways, the manuscript looks like a regular submission.
It might be worth noting, however, that
1. Rebus stories are usually very short (under 200 words and depending on the market, sometimes way under.)
2. Rebus stories have a small cast of characters.
3. The picture words are usually concrete nouns (not verbs or any other part of speech). And they are usually replaced with an exact picture. (In TURTLE, rebuse stories use a picture of an EYE for the word "I" but you won't see that in ANY other rebus story publisher as it is very confusing for young children.)
4. The replaced words are usually few but repeated (for example, you might use the word "mouse" repeatedly rather than having the child see a mouse, then a chipmunk, then a rat...keep the array of rebus pictures fairly small also.
5. Rebus stories normally have a twist or surprise ending.
Publishers for rebus stories include
Highlights
Ladybug (though they report being full at the moment)
Wee Ones (though only if you can do your own pictures)
Turtle
Note: Big Backyard uses a rebus story in every issue but they are done in-house.