Yes, you are right, "best" is my judgement in my particular situation at this point in time, and what you suspect is my "best" sums the situation up accurately.
Since I'm making the switch to a completely different format I just thought that I might as well do my whole library in one go so that I could have all my books on my new reader. However, your idea of converting only when necessary has a certain appeal to it and would make the unpack method less onerous.
Thanks to you all for your help and suggestions.