Batteries don't need to be broken in, they deteriorate with every cycle, although if they have been in storage for a while you might find that they perform a bit better after a couple of cycles.
I would definitely equalise before first charge, in fact even better (as someone else already mentioned in a similar thread) is to give the cells a small amount of charge (say 500-1000mAh) to get them off zero before equalising.
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