BizTalk 2006 introduced the concept of Application, allowing an easier management of deployments, by grouping together related artifacts as "logical applications". This concept has a somehow imperfect implementation, however.
Imagine I create an Application where I place shared schemas that are to be used by a set of Applications. One of these shared schemas is a property schema.
I now create a second application, and try to create a messaging filter in a send port for example: the properties in the shared property property schema in the other application will not be visible in the available properties list.
There is a way around this, as this is only an interface limitation. You can either use the binding files, or just start up Visual Studio 2005, open the BizTalk Explorer pane and add the filters you want to the appropriate send ports. BizTalk Explorer knows nothing about the Application concept.
If you create the send ports in BizTalk Explorer, they will be placed in "BizTalk Application 1", and you can move them into your application using the Admin Console (select > Move to Application).
Maybe a future version of the product could include a concept such as "dependent application", to work around this nagging limitation.