Hi there e Ujammie,
It sounds like you are wanting to sync these PDFs to your iPad from your computer. These don't automatically, you need to select them to sync over through your iTunes application to your device:
iBooks: Viewing, syncing, saving, and printing PDFs on iPhone, iPad, and iPod touch
https://support.apple.com/en-us/HT204365
To add PDFs to your iTunes library on your computer, drag and drop the PDF into your iTunes Book library. If you're using OS X Mavericks, drag and drop your PDFs into your iBooks library using iBooks for Mac.
To sync a PDF to iBooks on your device:
- Select your iOS device. (Learn more about syncing your data with iTunes.)
- Click the Books tab.
- Select Sync Books.
- If iTunes is set to sync only selected books, select the checkbox next to the PDF you want to sync.
- Click Sync.
You can use iTunes to back up your PDF files so they will restore to your iOS device after you update or restore your software or transfer information to a different device. If you use iTunes 11 or later to sync your PDF files to iBooks on your iOS device, a backup of your PDF will be automatically created. A copy of the PDF will be added to your iTunes Books library, or iBooks library if you're using OS X Mavericks.
Thank you for using Apple Support Communities.