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If you're converting to create production quality ebooks then you shouldn't really consider Calibre as your final tool regardless. If all you have is pdf then Calibre is a perfectly good tool to do the initial conversion from pdf to epub, but you should consider that a starting point, not the end point.
Unfortunately you're going to need to learn a little bit about the epub format, or find someone to do it for you. Creating commercial products that work on the iPad and on the Nook will take a bit of effort, and due to the fact that Apple doesn't conform to the epub spec in a number of ways means there may be some special handling required.
Do your conversion using Calibre, then edit the epub using Sigil. The epub sub-forum would be the best place to go for advice on creating a commercial grade epub and the people who regularly monitor those forums will have the best advice for you. There are a number of other threads where people have had to deal with Children's books, I recommend doing some searches and reading up on past experiences as a starting point.
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