If you have no need or plans to use Meeting Workspaces in your SharePoint site, you can skip this. You can always come back and go through this in case you do decide to use Meeting Workspaces. For those of you who are planning on using Meeting Workspaces, this post is for you.

By default when you create a Meeting Workspace site, it uses it's own master page called the mwsdefault.master.  This file is stored in the Global folder in the 12 directory (12\Template\Global) on the SharePoint web server.  This master page has some different code than the other master pages in SharePoint and from any base, minimal or default master page you are using for your custom branding.  If you ever decide to apply a custom master page to a meeting workspace, some of the workspace functionality will seemingly disappear. See below for an example of this.  NOTE: If you are using a Theme or an alternate CSS file for your branding, you can just override the styles used by the meeting workspace.  This post is not for you.

So what do you do? You take a copy of mwsdefault.master and combine it with your custom changes to create a branded master page that provides meeting workspace functionality. You can then safely apply this custom master page to your meeting workspace site while keeping unique workspace navigation and functionality.

OK, how do I automatically apply the custom master page to meeting workspaces?  Yup, here is the crummy part.  By default your new meeting workspace site will default to use mwsdefault.master and not your custom file. You have a few options here for how to handle this:

1. Manually apply the master page every time you create a site.  Not an optimal solution unless you only have a few sites you will be creating.  This is definitely not a viable solution if you are allowing your content owners the ability to create their own meeting workspaces (through the SharePoint UI or Outlook).
2. Create a copy of the Layouts folder in the 12 directory (12\Template\Layouts) and then make your changes directly to the mwsdefault.master page file. In IIS you can change the virtual directory your SharePoint site uses to the new copy. This is a safer alternative then directly editing the master page file on the server.  If you ever have any issues with your SharePoint site, you can easily switch the virtual directory in IIS to use the original Layouts directory.
3. Use a Feature to automatically set Meeting Workspaces to you your custom master page file. For this you will need a developer and knowledge on how to create Features and do Feature stapling.  I would suggest this as the best practice approach to solving this issue.

Meeting Workspace example:

1. Create a meeting workspace, in this example I created a Multi-page Meeting Workspace.
2. The Multi-page Meeting Workspace has 'Home/Page 1/Page 2' tabs across the top and options under Site Actions to Add Pages and Manage Pages. See a screenshot.
3. If you go into the Master Page Settings for the site, a warning message tells you that the master page setting is currently invalid (a.k.a. it isn't even using this master page) and the master page is "seemingly" set to default.master (or whatever master page you have set for the inheritance). See a screenshot.
4. Change the Site master page setting to default.master (or your custom master page file).  We are setting the Site master page (as opposed to System) because the content page (default.aspx) for the Meeting Workspace points to the custom master page field value in the database. Custom is the same as the Site master page setting.
5. Return to the meeting workspace. The 'Home/Page 1/Page 2' tabs across the top and options under Site Actions to Add Pages and Manage Pages has disappeared.  The reoccurring meeting navigation area has appeared, despite this meeting not having multiple instances. See a screenshot.