Yes you have to reject binary and need to submit app including in-app purchase again. You cant add IAP once you pressed "Prepare for Upload".
You may follow the directions below to add the IAP to the app version before uploading.
- Go to iTunes Connect
- Click on Manage your applications
- Click on the App
- Click "View Details" button
- Scroll down until you see an "In App Purchase" Section
- Add your In App Purchase to that version.
- Then ready your app for upload.
Once these steps are complete, the In App Purchase should automatically change from "Ready to Submit" to "Waiting for Review".
For more details, please check Apple about app statuses