For example:

$ export JBOSS_HOME=/home/kwills/git/wildfly/build/target/wf/
$ java -jar wildfly-10.0.0.CR1-SNAPSHOT/bin/client/jboss-cli-client.jar -Djboss.server.base.dir=standalone1 -Djboss.server.log.dir=log

[disconnected /] embed-server --std-out=echo

This should log to $JBOSS_HOME/standalone1/log

The properties available to override are:
jboss.server.base.dir defaults to jbossHome.getAbsolutePath() + File.separator + "standalone" ("domain" for domain servers).

jboss.server.configuration.dir defaults to "configuration"
jboss.server.log.dir defaults to log