IMHO Enterprise Manager as the only SQL Administration tool := Bad Practice
This is because you lack tracks to show what you did, except in the diagrammer. GUI's seldom leave tracks.
But, EM is great for noodling around in developer mode. I have had some of my best insights and "ah hah's!" looking at the code behind the EM's actions. It is easy enough to clip that SQL code out of the SQL window and paste it into Query Analyser, and this especially works well in learning mode.
The environment that I work in, is one that *all* production or pre-production jobs are scripted, almost everything is scripted. Why? Because you have an audit trail of the actions that you have performed against a server, (that is assuming that you capture the script outputs.....). We have used this technique for litigation support.
For example, imagine saying: "Why yes, Ms. Opposing Deposition Taking Attoney, as you can see here, the data was replicated from the server on this date and time to the CD which you have in your hand. And no, since the media was locked with the database and corresponding script outputs and logs, I can definitely state in my professional opinion that it is a true picture of the database at that point in time."
You get the point, I'm sure. I love GUI's to "see" complex concepts, but I'll always try to have that scripting and its output around for documentation.