OK the onboard SAS controller is a B110 or B120 which is for todays standard rubbish. The raid controller in the PCI-e slot is better and faster. Problem is that he is a raid controller. For using freenas with that controller you must create virtual drive on the raid controller and does get than presented to freenas. it works perfectly. but one thing will not work. Freenas never know when a drive fail. It will simply miss the drive. the only way to solve that issue is the raid controller out and a host bus adapter in. Some raid controller can be run as RAID and HBA.
Your disk in the front will be connected to the HBA and the HDD Backplane is a SAS Expander and all your drive will be presented to freenas. But before you start backup all your data on the drives..
The Reason why Freenas wants that ? Freenas is using software raid. and the HP DL3xx is using hardware raid.. And making hardware raid drives and presenting to the Freenas and than making software raid ist ending im disaster.
It is working and the performance is great with ZFS and Freenas but if one drive fails from hardware raid you got big problems turning up and it takes weeks to restore.
I recommend to you SAS controller out HBA in. And one thing will happen if you put the Intel NVMe inside. Than 6 fan will spin by 80% and more the entire time.. And you know they loud. reason is the air flow. the intel card is blocking the heat. And it does not matter if the intel card is left of the riser or right. the fans will spin up. they will work but i never did them to get to boot the windows os from. So i used it for database. for many read and write requests. HPE says it is not supported but this does not mean it is not allow to use it.
Some raid controller you also can flash the firmware and they turn into HBA.