I've been immersed in this subject for a couple off days, and yes it is quite baffling.
My understanding is that in your situation you would be liable for CGT on the full gain (less selling / improvement costs), as you only get PPR (Principal Private Residence) relief on one property, which would be your main home. You would have had to nominate the holiday home as your main residence for part of the time in order to get any relief on it, but this would reduce the relief you'd get on your main home. Of course if you never intend to sell your main home it might be worth doing that. A nomination can be backdated up to 2 years I think.