I, like Five, don't add track marks on the MD before transferring it. I find it easier to have the data in one long file, and then track it later. It makes any editing/mastering that needs doing so much easier, and far more consistant.
I think you can download the SonicStage (you want at least v4.3) update
here (it's been a while since I upgraded my version, but that site looks familiar. Once you transfer the files from MD, you use the 'Save in WAV format' option to make yourself a WAV file which you can edit. You can definitely do this if you record in PCM mode, and I believe you can do it in Hi-SP mode as well, but as Five mentioned, it's a compressed signal so saving it to WAV would involve bloating it out and wouldn't recover the lost data (as is my understanding).
I recorded Rush recently in PCM mode, and although the gig was three hours long, they had well placed breaks which meant I could do two disc changes. I'm still having issues with the levels, but I can get by with the auto-levels. It's something I'm still not complete clued up with.
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