I don't have the rules handy, but I think you replace an unnamed ship with the named one.
Yes, that is what typically happens with cards to be used for naval assaults and speed rolls to help catch (or make it harder to catch) Blockade Runners. But in the case of the CSS Alabama card, it says to place the named ship Alabama in a neutral European port. But my original post was directed at the situation where all 6 of the raiders were already on the board.
I came to the conclusion that the aforementioned card simply couldn't be played in that situation. Thinking about it more today, I thought of a follow-up question: If all raiders are on the board, but one is still sitting in a European port, could that counter be replaced with the Alabama counter?