First, I need to say that like any sophisticated program, you need to put a little time into Notion to see its full benefit. I've used Sibelius, (3 years), Finale (4 years) and Muse (1 year) and am very glad to have found Notion. Unless you're a manuscript librarian, I think all of these programs get in the way of the process of actually composing.
That said, you need to reassign the voices in each piece you import. I'm Mac rather than windows, but the process is pretty much the same. After opening your score, go to "Score Setup," either through the top menu or via the icon. You're page should look like the first few bars of your score with small ikons to the left of each part name. Simply click on the "gear" icon to change it's setting. Change the name from the midi instrument previously assigned to the Notion instrument you want to use. You will need to do this for each part. That's it. You may also adjust the display of the names at the same time V. for violin etc. Note, that like all decent instrumental libraries you will still need to do further editing on the score - inserting instrument specific marks as needed, for example Pizzicato, up and down bowing etc. for strings, muting and the like for various brass. You'll find these to the Right of the input menu when you're in edit mode.
Good luck. You're right though, Notion is a relatively inexpensive way of getting access to an instrumental library of decent quality. I think it's better than any other "inexpensive" packages out there (Garritan, etc). I use EastWest, but it's much, much more expensive. The only instrument that I was unhappy with was the concert Grand. You may like it or not, but there are many reasonably priced sampled pianos out there. I finally settled on Pianoteq, which in it's base configuration comes with several concert grands, + uprights, prepared instruments and a few harpsichords - each with multiple "mic setups." I strongly prefer it to either Notion's built in or EastWests instrument in the Symphonic packages.