Right now, we have Intelligence, Command, Pilot, and Temporal, as Primary Specializations and BOFFs may be trained in all four. The Secondary Specializations of Commando and Strategist cannot be taught to BOFFs at this time. Hopefully, one day they'll be made into Primary Specializations, as was done with Pilot. It's a sure bet that there will be more Specializations in the future.
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There is no retrain for specializations. You get basically infinite points for them as long as you keep filling the XP bar, so there's no real need for a retrain. Your captain's specializations (Edit: the category, not the points spent) can be changed in any "social zone" (sector space, ESD/Qo'noS/New Romulus, battlezones, places like that). It's all good.
Yeah, what @yoafro said. You'll earn enough Spec Points to fill in everything. But there's no way to reallocate points already spent. I believe you only need to spend a total of 10 points in any one Primary Specialization to begin training a BOFF in that Specialization, though.
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