You may need to disable the OpROM on the add-in card in the BIOS, but that's fine because you're not going to be booting from the 1TB HDDs anyway. Other than that, they should coexist fine.
The AHCI & RAID selection is specifically for the ESRT2 controller. As you mention you're running RAID 1 so you need it to be set to RAID. However, RAID includes AHCI capabilities. Does the ESRT2 controller plug into the add-in adapter? If not, how does the add-in adapter utilize the ESRT2 controller? I don't think you can specify AHCI for an add-in adapter within the S5500BC configuration. But like Dan said maybe disabling the OpROM for the controller would work.
I have a question though, are you using the S5500BC in a SC5650 chassis? If so you can use a hot swap hard disk drive bay to provide hot swap capabilities from the SAS/SATA controller on the baseboard. See the SC5650BCDP Technical Product Specification for more information.
If you're not using an Intel(R) SC5650 chassis, does your chassis offer a hot swap drive bay?
Another thing Dale. Be careful with the break a RAID, rebuild a RAID backup method. If during the rebuild, you have a failure on the second drive, that will cause data loss. A tested backup method to external media is the best way.