Thanks, guys. This still took me a little while to figure out, so here are a few clarifications for future readers of this thread...
(1) Type "everything /o" at the TakeCommand command line (as Scott stated) to open the Everything Options dialog box that you need to reindex the drives. You may also get to this dialog box by running the Everything.exe program itself (everything /e) and selecting Tools > Options.
(2) In the Everything Options dialog box, under Indexes, click NTFS. There you will see all your "Local NTFS volumes" listed.
(3) Select each volume in turn and check the "Include in database" checkbox for each one you wish to include in your searches.
(4) Once you have included all desired volumes, click the Apply button. The Xs in the upper right-hand corners of the dialog box and the main Everything window turn red while indexing is taking place, and the mouse cursor changes to a "busy" icon when your mouse is over either window. When indexing finishes, the Xs and cursor return to normal.
Note: I have 1.8 million files on the main drive on my system, but they're spread over four physical drives in RAID format. I also have two Western Digital 2 GB Passport USB drives attached, with about 400K files on each. It took about 2 minutes to complete the indexing of these three drives. I suspect that my time was longer than Scott's because the USB drives are obviously slower than my main drives.
(5) Click OK to close the Everything Options dialog box and searching should then work properly.
Again, thank you to Charles and Scott for pointing me in the right direction. I'm a happy camper again. :)