Entry Level Server question for a class I'm part of

[SRS-IT]

Have a ML310e that has Win08 R2 installed on a single drive (NOT in the LFF cage - NOT in an array - but plugged into the spare sata connector on the board.  Orignally we had the embeded smart array controller was disabled.  Now that our drives and trays are in we enabled the smart array controller again but my question is - with that enabled does the OS "HAVE" to boot from the smart array?  I know ideally it should - but we're going through a number of possible scenarios for differnt build types.  Thanks - SS