Buy Dan Erlewine's book on fret work. It will answer all your questions, and is a lot cheaper than bringing it to a repair shop to fix your mistakes (though you may still have to bring it in, as most people screw up there first few dozen fret jobs).
But to answer your question, you pull them, but you need the right tool to do it, and you can't buy it. Even the ones which are sold for this purpose (at least, the ones I've seen) don't have their faces flush, and so need to be modified.
But mostly, buy Dan's book, it will turn an impossible job (for an amateur) into only a nearly impossible job.
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"Cowards can never be moral."
M.K. Gandhi