Rodrigo,
The embeded controller is built-in and not removable, it is built into every C220/C240. The units are designed to work with PCIe and mezzanine array controllers when properly configured.
Once you install the PCIs controller, you'll need to do the following:
1) Move the mini-SAS conectors from the Motherboard to the PCIe LSI controller
2) Ensure the PCIe slot OptionROM is enabled in BIOS. (recent systems have their OptionROM disabled in unpopulated slots (from the factory). If you don't see the OptionROM during POST, then go back into BIOS and enable the PCIe slot OptionROM
3) While you are in BIOS, you might as well disable the Patsburg SCU array controller (The embeded array controller). It is of no use at this point as you've removed it's cables going to the HDD bay. It also causes confusion if you leave it enabled, as you'll see the LSI array configuration utility appear twice during POST. Once for the embeded and again for the PCIe LSI controller.
Dave
