You should ask about BOSS in the BOSS thread, but one of the first things people need to know to help you is what OS you are using. The separate partition thing is not important. I have done that in the past. Did you grab the separate DLLs download and drop them in the WINDOWS\Win32 folder (32-bit) or the WINDOWS\SysWOW64 folder (64-bit)?
Edit: These DLLs are new to the latest version of BOSS.
Part II of http://sites.google.com/site/oblivionpoinfo/walkthroughs/baininstallguide covers this.