The Black Freighter is an allegory that serves the dual purpose of putting you in a distracted state while the authors perform some sleight of hand while also parodying the verbose fashion in which epic tales boil down to "it was all a stupid mistake." You don't need to follow the Black Freighter. It's supposed to be over the top, empty, overly gory and vulgar and ultimately futile.
Phew. I quite liked it as a narrative device, both in creating a frame story that makes the main story seem more realistic and in its narrative parallels with the main arc. But they were always the parts I needed to read twice to understand what was actually happening. I wasn't sure if that was because it surpassed my English abilities or because it was meant to be that way.You don't need to follow the Black Freighter.
KB is right, you don't need to follow the Black Freighter - but I'll admit, it was only on this re-reading that I realised whose story the Black Freighter is meant to parallel (at least, I think I know). But further discussion of that realisation will have to wait for the full discussion. Or I could add a spoiler, to block it for those who haven't finished it yet. I think the Black Freighter parallels Adrian's story, especially the justifications of his monstrous actions; and the final futility in BF is much more obvious than in the primary narrative. Adrian only realises he is damned when Jon says "nothing ever ends".