Use WSDL2Java to generate the resource implementations
Generating an implementation with the WSDL you got from WSDLMerge is no different than in a normal Muse project -- in fact, it is probably a bit easier because WSDLMerge made sure to create a WSDL that abides by all of WSDL2Java's conventions. Simply run the following commands and WSDL2Java creates a project for each resource type.
$ wsdl2java -j2ee axis2 -wsdl JavaServerResource.wsdl -output java-server $ wsdl2java -j2ee axis2 -wsdl DatabaseServerResource.wsdl -output database-server
The two projects are in directories named java-server and database-server; each directory contains a complete Muse project and an Ant script for build and deployment tasks.
Look inside the JavaSource directory of each project and notice that each capability has its own Java interface and implementation file. In the interest of reuse, you may wish to extract the Java interfaces into a JAR that you can share between the two projects. The implementation file likely needs to remain separate -- J2EE application servers and database servers share many similar concepts, but the code needed to expose those concepts via Web services is likely be very different. The mapping of WSDL to a Java interface and then to an implementation class allows for a system wherein a client uses the exact same code to leverage a capability, regardless of what resource type it is part of and regardless of how that resource implements the capability internally.