The combined barrage is resolved separately for each unit in the company, so you would fire the barrage of Basilisk unit one first, followed by the same for Basilisk unit two, and then the sole barrage from the three Bombards (or the other way around if you prefer). You don't combine the barrage from all three squadrons together just because they are a company.
To this end, when the Bombards hit with their higher save modifier, you will resolve their damage separately compared to the Basilisks.
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