A screenshot might make your problem clearer... normally all you need to do is click on the brew or on the tome and it will automatically be filled in the next available slot. 

That being said, you should be very careful about spending skill tomes, because they are rare and should be saved for champions who will be viable in the long run. Especially epic or legendary skill books. For instance Shaman from the login rewards is very useful early on, but when you get a bit further in the game you'll almost never use her again and if you maxed out all her skills with tomes, you'll regret it because you'll be needing epic skill tomes for much better champions. I speak from experience on that...