Hello ,
Welcome to the Apple Support Communities!
I understand that you would like to sync your iBooks collections from your computer to your iPads while keeping them in their collections. To accomplish this, please follow the steps outlined in the attached article.
Sync iBooks between devices - Apple Support
If you start reading a book on one device, you can pick up right where you left off on another device. Collections, highlights, notes, and bookmarks sync across all of your devices. Select these settings to sync:
- On your Mac, open the iBooks app and select iBooks > Preferences > General. Then, select "Sync bookmarks, highlights and collections across devices." This setting is on by default.
- On your iOS device, go to Settings > iBooks. Then, select Sync Collections and Sync Bookmarks and Notes. (In iBooks 3.2 or earlier, select Sync Collections and Sync Bookmarks.)
Have a great day,
Joe