You should set inputs.conf with index=<indexname> so that the data coming from this input will end up destined for the specified index. If the data is ending up in two different places, perhaps the data is older and from a point where you hadn't defined the index where you wanted to see the data? If that is the case, you can't selectively move data from one index to another, so your data will remain in the original index. If you set up this input and you see current data ending up in two indexes, you've probably got a transform to route the data into another index someplace in your configuration.
You can look at your btool output to determine if any of these things is occurring. Run the following command from $SPLUNK_HOME/bin/ on the indexer if you're using a UF/LWF, or on the heavy forwarder, if that is what your using.
'splunk cmd btool inputs list --debug > ~/inputs.out'
'splunk cmd btool props list --debug > ~/props.out'
'splunk cmd btool transforms list --debug > ~/transforms.out'
