@vhayman: Sorry I missed your comment and did not reply earlier.
There is a way to customize how the gerenated Sql code looks like. You can create a custom element in the CSDL that will have CopyToSSDL attribute in edmx v2 namespace (this is actually a bug since even if you are using edmx v3 you still need to use edmxv2 namespace - we have a bug on this: http://entityframework.codeplex.com/workitem/702). Then you would create your custom T4 template (based on the one that is included in VS - SSDLToSQL10.tt) that generates the Sql code so that it understands the extended properties and generate Sql accordingly. I found a walk through that does it:
Having said that extending the EF designer this way is obscure and difficult. I created a work item (http://entityframework.codeplex.com/workitem/807) for adding support for indexes in the EFDesigner.
Thanks,
Pawel