By the looks of the syntax there you do not have to change the drive to a primary one.
From the link
"apmtimer [options] /dev/device"
We could cover Linux directory naming (short version is everything, right down to the programs running, is represented in a single unified file system unlike windows which can have a thousand different drive letters) but I will not as for this if you go into the dev directory on the root of the file system and then it will be in there somewhere. If it is USB then it will probably be SDA, SDB, SDC... depending upon how many external drives there are. The numbers after tend to be for different partitions on it.
Alternatively if you have something like gparted installed it should be fairly easy to figure out what is what (select the drive in the top right corner).
I should note though that also on the link
" Compatibility with SATA-to-USB adapters has not been tested." and it could well get in the way -- a lot of adapters might not implement the full SATA spec and this is one of the sorts of rarely done things that might be skipped.
