When I first started IT, I didn't understand the need for many glossaries. I didn't even have a drug glossary. I had one main glossary, one surgery, one cardiopulmonary and one radiology. It wasn't long before I realized it would be much faster to subdivide the surgery glossary and make new glossaries for the specialty surgeries we do at our hospital, including orthopedics, OB-GYN, ENT, and urology and leave the regular surgery glossary for the cholecystectomies, appendectomies, colonoscopies, etc. It wasn't long either before I realized I needed a separate drug glossary to keep all my drugs together. Then I realized cardiopulmonary needed to be separate glossaries for EKGs, EEGs, and sleep studies. Later on I realized I needed a separate glossary for practitioners, so now if I type drsmi, I get Dr. Smith, Dr. John Smith, or John Smith, MD, for example, with a display noting his specialty if needed. So to make good glossaries, I would advise to avoid the temptation to limit yourself because you think it is "easier," and really go for specialized ones for those report types that need them. If you are concerned about having different words/phrases expanded differently in all those glossaries and want some continuity, an "always there" glossary which is consistent and can be included with every other glossary is a great option for those expansions you want the same everywhere.
I think with the command option now, it is important to create a quick way to enter a new item in the glossary (I use "ad" which brings up the add to the glossary screen quickly) on the fly, and I also subscribe to Drugs.com e-mail list which e-mails me meds as they are approved, and I take a few minutes each morning before work to add those to my drug glossary if I receive an e-mail. (I also use the great display feature to note the indication, e.g., glaucoma, for each new drug, since they are all unfamiliar to me as of yet.) Every time during transcribing when I come across a new drug, after verifying it, I make an entry into my drug glossary. IT7 has made it so easy to add on the fly as well as a cinch to switch glossaries quickly, there is no excuse for not adding these on a regular basis.
Of course, compile, compile, compile! Not using this feature is like having a top-of-the-line sewing machine and only using a straight stitch and ignoring all the other wonderful stitches that are there!
All these things I have gleaned in the last few years by reading the IT forum here, asking questions here (which have always been answered fully and promptly), "playing" with IT on my own time, and taking some time in making or adding to new glossaries and doing compilations. Well worth the investment. In the end, you will have an excellent, customized set of glossaries tailored just for you and your account(s).