SQL 2012 :: Setting Up Transaction Replication In Test Environment From Production

Setting up Transaction Replication in test environment. I am willing to bet that most of you take a production backup (if so, how, and using what?), restoring the database to your test environment, then running a snapshot to your subscriber and away you go.

But perhaps you take a backup of your publisher and subscriber, if so, how do you know there are no inconsistences because there were transactions sitting on the distributor?

What do you do if you have additional indexes on the subscriber for reporting, that are not on the publisher?

Here at work we are having issues with getting consistent databases set up with T Rep, missing rows, duplicate keys at subscriber etc. How to avoid these issues.