Indexed drives
HKLM_SW_AD\Agents\File\Roots is where you can add or modify the ability to index a drive, as a whole or partial, and what directories to exclude.
The first branch starts count at zero for the first drive you mention to AD (I haven't tried to find a maximum amount of drives to add). Opening the first branch 0 shows 3 values: "Name", a STRING with the value "Documents", "Path", a STRING with the value of the drive, say "C:\" and "Partial", a DWORD with as value zero or one according to exclusion settings.

Adding a drive
Add a key (NAME must be a number) under HKLM_SW_AD\Agents\File\Roots. Expand and add the values: "Name", value is "Documents", "Path" value of added drive and "Partial" (zero or one).

Adding a directory to the exclusion list
Add a key with NAME "Exclude" to a drive branch key under HKLM_SW_AD\Agents\File\Roots\(NUMBER). Expand key and add a STRING with NAME (number, starting from zero) and value of the directory you want excluded in LFN-like format, like "X:\groups\Security Settings\FW-1 Application Users\Application Data". I haven't tested for restrictions like adding a directory on a different drive, but if you feel adventurous you could try not complying to the directories-per-drive stylee :-]