As of #3527, Beat versioning is added in the index template by default:

beatname-%{[beat.version]}-%{+yyyy.MM.dd}

Notes:

1. If two Beats are running of different versions (5.x and 6.0) or we upgrade from 5.x to 6.0, then there are:
   indexes: beatname-* and beatname-6.0.0-*
beatname template that applies to all beatname-* indexes
   beatname-6.0.0 template that applies to beatname-6.0.0-* indexes.
   As a result, the beatname template applies for beatname-6.0.0-* indexes as well, so we need to set a higher priority to the beatname-6.0.0 template to overwrite the settings in 5.x.

2. The difference between the template used after upgrading 5.x to 6.0 (master) and the template after a fresh 6.0 (master) installation is the following:

 diff metricbeat-6.0.0-alpha1-2017.02.23-without-upgrade metricbeat-6.0.0-alpha1-2017.02.23
8a9,11
>         "_all": {
>           "norms": false
>         },
4130a4134,4136
>         "_all": {
>           "norms": false
>         },
8260c8266
<         "creation_date": "1487849241372",
---
>         "creation_date": "1487848996929",
8262c8268
<         "uuid": "jYJf-6BJTLST07ZpN8TwMA",
---
>         "uuid": "tv36cO3QQKije38f_xtw_g",

Waiting for #3603 to be merged, so we can do the implementation directly in Go.