Currently I have a zookeeper multi solr server, single shard setup. Unique ids are generated automatically by solr.
I now have a zookeeper mult solr server, multi sh
There is no way you can route your documents to a particular shard since it is being managed by the zookeeper.
Solution to your problem is that you should create two collections instead of two shards. Use your 1st collection with two servers and 2nd collection can use the third server and then you can send your updates to particular servers.The design should look like
collection1---->shard1---->server1,server2
collection2---->shard1----->server3
This way you can separate your indexes as per your requirement.