I am actually a bit confused as to why the A2000/500s have 1 and the 3000/4000s have 2. Is one for the onboard HD controller and one for the System?
No. Both have the same data (or can have, they usually are a bit different, A3000 has SCSI drivers, A1200/A600 ones have IDE and PCMCIA drivers, A4000 ones have IDE drivers, A4000T ones have IDE and SCSI drivers etc).
If so, do they each have the same ROM image and only use the portion that they need?
A500/A600/A2000/CDTV use 16-bit access, while A1200/CD³²/A3000/A4000 use 32-bit. For the 32-bit ones the ROM is split to two portions so the access can be overlaid for better performance.
CDTV and CD³² actually were a bit special, they both had more ROM than other systems. For example CD³² had 512KB (the normal ROM) and 512KB (CD drive drivers, and other built-in driver software).