I remember it being easy before, but I don't remember exactly how to do this since my return. A little help?

Go here: Iltallo He will ask for coda caves crystals. Choose your pet wisely though, you can't undo it if you click on the wrong one.

Thanks! These new maps can get very confusing.

there's a brand new FAQ Guide, it's linked right now on the News Page. If you check it out, this will help you get back up to speed. It will help with the confusing things, and also has how to get different color pets.