Two RAID controllers on one server should be fine, if you have two backplanes, although you should be able to connect all your HDDs to one controller through expander backplanes... You can't connect two controllers to one backplane.
As for link speed, if you're using 3Gbps drives, everything will be fine. But if you're using 6Gbps drives, since the RAID controller negotiates link speed with drives not the backplane, it may try to establish link at 6Gbps. Now since the backplane supports 3Gbps only, you may have a problem. The workaround is to limit the hard drives to 3Gbps, most likely it's via a jumper on the drive itself.
Another reminder: Server Products - Can I mix SAS and SATA hard disk drives?