Over a year later I know, but hopefully useful to somebody: you can accomplish this by setting the properties inside your Spring context xml:
<bean name="schedulerFactory" depends-on="flyway" class="org.springframework.scheduling.quartz.SchedulerFactoryBean">
<property name="quartzProperties">
<map>
<entry key="org.quartz.threadPool.class" value="org.quartz.simpl.SimpleThreadPool" />
<entry key="org.quartz.jobStore.useProperties" value="true" />
<entry key="org.quartz.jobStore.class" value="org.quartz.impl.jdbcjobstore.JobStoreTX" />
<entry key="org.quartz.jobStore.driverDelegateClass" value="org.quartz.impl.jdbcjobstore.StdJDBCDelegate" />
<entry key="org.quartz.jobStore.tablePrefix" value="QRTZ_" />
<entry key="org.quartz.jobStore.dataSource" value="qzDS" />
<entry key="org.quartz.dataSource.qzDS.jndiURL" value="java:comp/env/jdbc/${jndi.dataSource}"/>
</map>
</property>
<property name="applicationContextSchedulerContextKey">
<value>applicationContext</value>
</property>
</bean>
Notice I've put most of the JobStore-related properties in here as they seem to need to be in the same place. There is still some other configuration in the usual quartz.properties file.