Hi,
If I create a SEP 12.2 package with only AV and AS feature will this package overwrite the current features or it will still keep the existing features(ALL Features)?
--> It will overwrite the current features.It won't keep all existing features however reboot may required to show desired results.
You can refer this article to know more about it.
https://www-secure.symantec.com/connect/articles/sepm-121-auto-upgrade
Also to upgrade the SEPM you can refer this article:
Upgrade process from SEP 12.1 RU1 MP1 to SEP 12.1 RU2
https://www-secure.symantec.com/connect/articles/upgrade-process-sep-121-ru1-mp1-sep-121-ru2