The only thing I did when I first built this system and started it up in non-RAID configuration was go into the bios and set boot devices (choose ATA100 controller, not IDE0), and then go into the HPT370 bios (control-H) and set the boot drive. While you're in the controller bios, make sure that the controller is running both hard drives in DMA mode 5 (ATA100).
If you want to know how to set it up as Windows/Linux dual boot without messing with your Windows MBR, just send me a PM and I'll explain how I did it.
PS - I'm not sure if your Promise controller has these options, but if it does, you can use it as a boot controller.