Hi Jonathan,
You can do several things - you can use the Enharmonic tool to correct the notes (Shift+E), you could click-select the note and use Shift+Up or Down arrow - this will give you chromatic transposition and you can move the note up or down untill you get the right pitch, or you can try Transposing the passage to another key (like A Minor) and then transpose it back to Eb minor (not sure how this will go, but just a suggestion to try).
However, another idea is to avoid the MIDI route all together. I'm not sure about Logic, but I know Cubase supports MusicXML export. If Logic does, I'd highyl recommend using MusicXML files because the level of accuracy is much higher (this is true for any scoring application, not just NOTION). This will also solve the tie issue...
Hope this works out.
Lubo Astinov