Problem with indexing

Okey, third time's the charm.

I want to use elasticsearch to search a mongoDb, and I've manage to make the connection (using monstache) but the dynamic indexing does not index the documents right. I have one db with lots of objects, and two arrays with objects within it.
But the problem is that when I use discover it doesn't present the data right (like in the database) which makes it hard to have an easy overview of what you are looking for.
I have already started a topic on this twice, and got the advice to start a topic and using Logstash to make the connect (I used monstache cause I thought it was hard to find documentation that was updated about syncing mongodb and elasticsearch)

I have tried using index templates, which only makes about 2 million more documents (because of the Nested datatype)
Please explain if and HOW it is possible to ensure the documents are indexed right so it presents itself the way it should.

So for example

param (array)
-- obj 1
---- index 1
---- value 2
-- obj 2
---- index 3
---- value 4

but what it does now is

index 1,3
value 2,4

these are fields that contain a lot more than these two values so it's not really optimal for them to group if you want a quick overview of the values.

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