Are you saying ImportOmatic is creating duplicate records in the Raiser's Edge? Or are you saying you have a lot of duplicate records and ImportOmatic shows them to you when you import and you want to resolve them. If the first one, post a message with specifics about it here, if the second one, download and run MergeOmatic from here to analyze your duplicates.
Mostly the issues are within my profile or duplicate configuration and a quick tweak to the profile fixes the issues.
However, I did notice a couple of times in my import that a person is an exact match, but they do not show up in the search result, so, I search for them directly and the match score is coming up as 0. It is not a spouse record or a non-constituent record. It is currently being reviewed by the support team.
I came across your posting and found it interesting about "MergeOmatic is great because you can run a duplicate search based on a query". Are you talking about running this before you import the data or after you import the data.
When import into RE duplcate records are showing up.
Or visa versa
How to get all duplcates out before and after merging records from web.