One of the questions often asked is what the default management pack is for. Especially when you tell somebody they should not save overrides and stuff in there, while it is always right there as the first selected management pack to save something to! Quite logical that this confuses people and that is likely that there will be overrides/groups and other items in there after some time. One of the problems is that with every override you create more and more dependencies on the default mp, so in order to delete any mp you will probably run into SCOM complaining about the dependencies. Also it creates a lot of clutter and you will not have an overview anymore of what is where.
The first tip would be to rename the default management pack. In the SCOM console go to Administration pane and find the Management Packs entry in the left of the screen. Next find the Default Management Pack. Double click it to get the properties. In the Name field you can change the name there. Usually I add something like (DO NOT SAVE HERE!!) either before or after the name. At least it is a visual reminder you/they should not save stuff there.
For sure it will happen that stuff gets saved there so here is an article from Kevin Holman explaining more about this MP and how to clean it again:
http://blogs.technet.com/b/kevinholman/archive/2008/11/11/cleaning-up-the-default-mp.aspx
Also a very nice one is a custom mp from Jonathan Almquist that monitors the default mp for changes:
http://blogs.technet.com/b/jonathanalmquist/archive/2008/11/12/monitor-default-management-pack.aspx
Keep your default mp clean.
