Different document types (within one project) require different schemas. If the documents share common XML types, they should be written once, in a separate schema file, and re-used from there wherever they are required. The common definitions could be assembled into a namespace of their own, to avoid any conflicts with type or element names in the schemas where they are used. The XML schema snippets given below illustrate this approach.

<?xml version="1.0" encoding="utf-8"?>
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
            targetNamespace="http://astronomy.org/common"
            xmlns:ast="http://astronomy.org/common">

  <xsd:complexType name="BodyType">
    </xsd:sequence>
      <xsd:element name="name"   type="xsd:ID">
      <xsd:element name="mass"   type="xsd:float">
      <xsd:element name="radius" type="xsd:float">
    </xsd:sequence>
  </xsd:complexType>
</xsd:schema>

<?xml version="1.0" encoding="utf-8"?>
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema"
            xmlns:ast="http://www.w3.org/2001/XMLSchema"
            targetNamespace="http://astronomy.org/solarsystem"
            xmlns:ss="http://astronomy.org/solarsystem">

  <xsd:import namespace="http://astronomy.org/common"
              schemaLocation="common.xsd"/>

  <xsd:complexType name="MoonType">
    <xsd:extension base="ast:BodyType">
    </xsd:sequence>
      <xsd:element name="planet" type="xsd:IDREF">
    </xsd:sequence>
  </xsd:complexType>

  <xsd:complexType name="PlanetType">
    <xsd:extension base="ast:BodyType">
    </xsd:sequence>
      <xsd:element name="moon" type="ss:MoonType"
                   minOccurs="0" maxOccurs="unbounded"/>
    </xsd:sequence>
  </xsd:complexType>
</xsd:schema>

It should also be noted that it is not necessary to have one schema file for each document type. Any top-level element definition (by some xsd:element schema element) is a candidate for a root element, and you may have as many as you like within a single schema. The previous schema snippet might be extended with the following element definitions:

<xsd:schema ...>
  ...
  <xsd:element name="planet" type="ss:PlanetType"/>

  <xsd:element name="solarSystem">
    <xsd:complexType>
      <xsd:sequence>
        <xsd:element name="planet" type="ss:PlanetType"
                     maxOccurs="unbounded"/>
      </xsd:sequence>
    </xsd:complexType>
  </xsd:element>
</xsd:schema>

Marshaller m = context.createMarshaller();
ObjectFactory of = new ObjectFactory();

// Create a single planet instance document.
PlanetType planet = of.createPlanetType();
//... Add attributes and moons
JAXBElement<PlanetType> jbe = of.createPlanet( planet );
m.marshal( jbe, System.out );

// Create a solar system.
SolarSystem sol = of.createSolarSystem();
//... Add planets.
m.marshal( sol, System.out );