Yeah, there is a way.
Assuming:
xsd/common/common.xsd
xsd/foo/foo.xsd
In the common directory place common.xjb:
<jxb:schemaBindings>
<jxb:package name="mypkg.common">
</jxb:package>
</jxb:schemaBindings>
In the foo directory place foo.xjb:
<jxb:schemaBindings>
<jxb:package name="mypkg.foo">
</jxb:package>
</jxb:schemaBindings>
In the build.xml file, create one xjc task for each:
<xjc destdir="${app.src}" readOnly="true" package="mypkg.common">
<schema dir="${app.schema}/common" includes="*.xsd" />
<binding dir="${app.schema}/common" includes="*.xjb" />
</xjc>
<xjc destdir="${app.src}" readOnly="true" package="mypkg.foo">
<schema dir="${app.schema}/foo" includes="*.xsd" />
<binding dir="${app.schema}/foo" includes="foo.xjb" />
</xjc>
You need to make sure that common.xsd has a targetNameSpace that is different from foo.xsd's targetNameSpace.