Can I make the mvXCell-8i as the main processor but not the secondary one in preprocessor mode?

mvXCell-8i, mvXCellBox

No. This will not work. You need to start the mvXCell-8i either as a secondary card on a PCIe bus or in "root-complex" mode as the primary card. You can change modes only with a jumper on the board and then rebooting the mvXCell-8i. Yes. We can provide a box (mvXCellBox) containing mvXCell-8i, PCIe backplane, empty slot for another card and a power supply.