Depending on your budget, there are several packages I would recommend to do what you're talking about.
First is Audacity, which is open-source, hence free for non-profit use. For basic editing it has all the features you would need, as well as many you wouldn't [like multitracking].
Second would be Sound Forge, a mono or 2-track editor that I've been using since before 1.0 came out [around 91 or 92] and can highly recommend.
Third would be Cool Edit, which I've never liked the interface of though it does an excellent job with transcribing, editing, etc.
There are also some utilities that apparently allow your NetMD to transfer track markers by USB while doing an analogue dump. I'm not in the know on this, but hopefully someone else here spots this and gives you that info.
Cheers,
D.