If you both use the same iTunes account you can download the books to each other's devices for free. If you use different iTunes accounts things get sticky. You can try singing in and out of each other's account in the iBook Store, and that may work; but you'll have a heck of a time keeping track of what book was bought with what account.
If you have two accounts, this is what I would do. Pick one account that you both agree to buy all book with. Sign into the iBooks Store on both iPads with that account. As long as you do that you'll be able to see all your books in the Purchased section of the iBooks Store, and download the ones you want on each iPad.
You can sign into the iBooks Store at the bottom of most tabs. There will be a button with your Apple ID. If it's not the Apple ID you want to be purchasing books with, sign out, then sign back in with the right one.
This will only affect the iBook Store. iTunes and the App Store have to be signed into separately; though you might want to consider doing the same thing so you can share apps and music as well.
BTW, the EULA specifically permits sharing Books, Apps, and music between family members; and they would probably be the only ones you'd want to trust your Apple ID to anyway.