So far there is no packaged upgrade path from 1.x to 2.x
I did upgrade both system and Ebox in the past with no major issue using apt (even running Ebox on non LTS) but if your system is in prod, I would suggest to stick on the only reliable approach (at least for what I understand) that is to reinstall 2.x from scratch and then import data once you have set up the new Zentyal platform.
I did it once with Zentyal acting as internet gateway (meaning few data aside mail). In order not to be impacted with incoming mails during migration, I changed settings on my external router so that port 25 on Postfix was not exposed to internet, then reinstalled Zentyal, configuration and then restored mail data that's it (for what I remember)
Of course you have to configure Zentyal with same accounts. I have quite few so I did it manually.
In case you have significant amount of account, it might be interesting to export LDAP entries (users and groups) to LDIF and then import again.
@Zentyal team: has DIT changed between Ebox 1.x and Zentyal 2.x (which would prevent smooth LDIF export then import). What's about schema?