Ah, sorry I misunderstood you question.

When we deploy our software, one of the steps for the client is to run an SQL file which performs all the DB modifications. Its done this way as we dont have direct access to their database and it means we can just ship them an SQL file which run on their own servers.

There is no reason not to use a GUI tool if one is available, but I think its also good to understand the underlying SQL. Its very easy to press a button in a GUI without actually realising what its doing.

Some people, the sort who know the commands already - can probably type "alter table myRecords add column id int auto_increment first, add primary key(id);" before the splash screen for Enterprise Manager has disappeared.

Ah ok, for upgrade scripts that kind of makes sense. I get the feeling a lot of these types of questions are from learners though, I don't think it's something people actually need to learn until they do - their time would be better spent on other parts of SQL.

Also, you can tell someone how to do it without having to have the same version of the same database manager GUI. Likewise, if you are googling to solve your own problem you have a much better chance of finding a solution that will work on your setup.

On larger tables an alter table, alter/add column command probably wouldn't be the best way to modify the table as it might cause page splits and data fragmentation (affecting performance).

When you use the GUI the SQL Server IDEs do an ok job at mitigating this behind the scenes - they'll create a new table with the new schema, transfer the data from the old table, then rename the tables.