indexing for disk psrtitions/ removable disks

Once the separate partitions are mounted at a point in the filesystem, they all become just part of the filesystem, so their physical location is much less important. I normally use the command line "locate" for a pretty quick search of the filesystem. I see the gui "places" windows have a search bar, but I find that to be much slower than the locate command.

I can access all files & folders in my disk partitions/ removable HDD without having to perform any operation after a boot-up, if that's what you mean.

I'm using a program called 'Disk Utility' (ver 2.3). I assume this app automatically mounts all my drives on boot-up?

But 'Gnome Do' refuses to list any files stored on a drive other than the Ubuntu root directory.

Additional Info:
I have another program called 'Tracker Search Tool', which detects files/ folders on all my partitions & external drives automatically.

But I'd really like to use something user-friendly like Gnome DO, if only it indexes all my drives.

There is only one root in Linux, and applications like Gnome Do and Tracker only deal with the filesystem, not unmounted disks. However, Gnome goes overboard mounting every partition it can see, sticking them in /media/... Gnome ignores the old method of partition mounting which is to list the partition fstab. Gnome ignores the 'noauto' option to explicitly suppress this automatic mounting when listed in fstab. You can turn off ALL Gnome automounts, but I tend to like having my usb thumbdrives mount automatically. The only way I have found to reliably suppress the Gnome automounting is to explicitly list the partition in a mount location OTHER THAN /media (like /mnt) with the noauto option.
  Now indexing is not instantaneous, so I can believe if you do leave the drive plugged in (and mounted of course), your tools will not see the files. I think there is a database somewhere that the command location uses, so if that is the way tracker works, even a partition which had been indexed would be removed from the database the next time an update was run. Maybe some tool exists which uses a distributed database, so the part for a partition is actually on the partition, but I don't know of any. Undexed searches are slower, (like the ones in nautilus, (used by the places tab), but do not require the disk to be present for any period of time (to perform indexing).