You may first start payara-micro with --rootDir path option. Payara treats this dir as working, so it creates `config' dir there. Then just edit domain.xml file as you need and start payara-micro again. All resources you create will be available at you beans as usual. For example you may add some properties like this:
...
<resources>
<jdbc-resource pool-name="DerbyPool" jndi-name="jdbc/__default" object-type="system-all" />
<jdbc-connection-pool is-isolation-level-guaranteed="false" name="DerbyPool" datasource-classname="org.apache.derby.jdbc.EmbeddedDataSource" res-type="javax.sql.DataSource">
<property name="databaseName" value="${com.sun.aas.instanceRoot}/lib/databases/embedded_default" />
<property name="connectionAttributes" value=";create=true" />
</jdbc-connection-pool>
<connector-connection-pool max-pool-size="250" steady-pool-size="1" name="jms/__defaultConnectionFactory-Connection-Pool" resource-adapter-name="jmsra" connection-definition-name="javax.jms.ConnectionFactory"></connector-connection-pool>
<connector-resource pool-name="jms/__defaultConnectionFactory-Connection-Pool" jndi-name="jms/__defaultConnectionFactory" object-type="system-all-req"></connector-resource>
<context-service description="context service" jndi-name="concurrent/__defaultContextService" object-type="system-all"></context-service>
<managed-executor-service maximum-pool-size="200" core-pool-size="1" long-running-tasks="true" keep-alive-seconds="300" hung-after-seconds="300" task-queue-capacity="20000" jndi-name="concurrent/__defaultManagedExecutorService" object-type="system-all"></managed-executor-service>
<managed-scheduled-executor-service core-pool-size="1" long-running-tasks="true" keep-alive-seconds="300" hung-after-seconds="300" jndi-name="concurrent/__defaultManagedScheduledExecutorService" object-type="system-all"></managed-scheduled-executor-service>
<managed-thread-factory description="thread factory" jndi-name="concurrent/__defaultManagedThreadFactory" object-type="system-all"></managed-thread-factory>
<custom-resource factory-class="org.glassfish.resources.custom.factory.PropertiesFactory" res-type="java.util.Properties" jndi-name="myconf">
<property name="some.my.property" value="some.value"></property>
</custom-resource>
</resources>
(see custom-resource tag)
Then just inject it into you bean:
@Resource(type=java.util.Properties.class, name="myconf")
private final Properties parameters;
Also you may specify --domainConfig file to keep configuration anywhere you want.
Use --help to see full options list.