legendaries are limited time but you will always be able to get more rare candy so i don't really think there is a bad choice on what to spend on (though obviously wait till that boss ends before using candy incase you get something better). i personally level the best of each legendary i've caught to 30 unless it was completely useless (suicuine) or terrible iv's and you have something else to fill it's role (in your case kyogre, though even a poor one should beat gyarados).
you can afford to drop a lot of candy on anything IMO and keep 100ish in reserve for when you get a mew2. as awesome as metagross looks it doesn't seem to be much use so personally i'm holding out for a really good beldum before evolving. best legends by far are kyogre and groudon followed by raikou, i'd not take any others past 30 unless fire or ice becomes useful in raids.