Personally, if you've already seen the first Negima anime, it's okay to skip the first three volumes (which were covered decently in the anime) and start with volume 4 (the start of the Kyoto arc). As Charred Knight pointed out, the Xebec version gutted a lot out of the anime version of the Kyoto arc (especially the one thing that really got me into the story, Nodoka's Pactio).
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