How are you upserting timestamps? The phoenix.query.dateFormatTimeZone config property only affects string parsing or the TO_DATE function (docs on this are at ). If you're using the TO_DATE function, it's also possible to supply a custom time zone in the function call (docs on this are at ).
Regardless, if you want to use this setting, you need to update the hbase-site.xml on the client machine where you're connecting to HBase/Phoenix. This configuration file will typically be in /etc/hbase/conf, although if you're using Cloudera Manager (or probably some other cluster management software) the hbase-site is automatically overwritten by CM, so you'll need to configure this within Cloudera Manager itself (via configuration settings called "Gateway safety-valve", or something along those lines).
In any case, there are often issues due to the odd way in which JDBC itself handles (or doesn't handle) timezones, so the best way to resolve this issue is probably for you to post some examples of the statements you're running, what output you're getting, and what you would expect instead of what you're getting.