If the new template has the same name as the old, you can overwrite the new with the old. Your configuration, however, will not be updated until you re-deploy the iapp. Enter the iapp via the "Reconfiguration" tab and click "Finished" to re-deploy.
If the new template has a different name, as most F5 updates do, you can import the new template and "re-parent" your iapp. For example, if you are using the template called and you are updating to f5.microsoft_exchange_2013_cas.v1.5.1, then you should (1) enter the iapp reconfiguration screen, (2) click "change" next to the template name, (3) choose the new template, and (4) click "Finished" to r then you should (1) enter the iapp reconfiguration screen, (2) click "change" next to the template name, (3) choose the new template, and (4) click "Finished" to re-deploy the iapp using the new template. If there is something that you do not like about the new version, you can simply re-parent back to the old template.