I figured out a neat way to help fill out your encyclopedia.
There is a way to combine and add monsters to your book without actually "using up" the monsters.
1) combine two monsters that make a third new type.
2) Viola will immediately add the monster to your book
3) You are given the choice to take the monster home. If you refuse, both parents reappear back in the deep freeze, but the baby is still in the encyclopedia!!
4) this works even better when you already have your maximum number of monsters. You begin to combine, but you are told to pick one of your active monsters as the second parent, since you are full already. You can repeat the above with any of your trained monsters, and not lose them unless you take the child home.
This is great for filling holes in the book, but I am really going to wait until I have some trained retirees and some semi trained replacements. If the encyclopedia saves added techs and other combo bonuses like in MRA2 this could be a major discovery.
I hate to say it but I don't really think this was intended by Tecmo. In my mind it falls into the category of a minor exploit at least, and a major exploit if combo bonuses transfer to encycopedia entries.
Now, book entries are always the same, so these entries won't be any better than if they were shrined from CD, but it is a way to fill your book, and save the parents for the combination you really want to use them in.