I just uploaded a new version to hackage. This improves the heuristics for guessing the right module quite a bit, and adds a local config file where you can prioritize or de-prioritize packages or module prefixes. It's also a bit faster.
From the hackage description:
A small standalone program to manage the import block of a haskell program. It will try to add import lines for qualified names with no corresponding import, remove unused import lines, and sort the import block according to some heuristic you can define. This only works for qualified imports! Unqualified imports are left untouched. It's most convenient if bound to an editor key. Recent major changes: version 1.0.0 Change name from FixImports to fix-imports, which is more unixy. Change ghc-pkg parsing from String to Text. It's noticeably faster. Add a more flexible system for prioritizing imports. When there are several possibilities for a module name, they are all given to a single function to decide. The config file moved from fix-imports-priority to .fix-imports and can now specify sort orders for packages and modules by prefix. Make -i includes for non-existent dirs ignored instead of causing an error.