Hello DerkGB,
1. The Ramilies is effectively a squadron of 4 spacestations with bonus basilica weaponary. So the boarding player may choose how many quadrents are boarding. Note: the Ramilies could board back in the following turn with all quadrents as it will still be in contact at the end of its movement phase (is it really worth it though?).
2. Treat each quadrent individually. So 12 dice back and only that quadrent may be damaged.
3. Well as the space hulk is also a defence 2d6.
Cheers,
RayB HA