So yes summary indexing will create a new host, source and sourcetype field for that data that has essentially been newly indexed into the summary index you just created.
You can either just use different field names for the host, source and sourcetype fields (i.e. orig_) or remap them using the option under the Summary Indexing in the UI.
I've always found the best way to validate and test a new index is to use the | collect command to ensure everything looks OK before setting up the job. The Summary Indexing option in the UI really just uses that | collect command anyway.
Check out the docs for more info:
http://docs.splunk.com/Documentation/Splunk/6.4.1/Knowledge/Usesummaryindexing
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