Yeah that sounds about right. If you don't want to loose the transitions between the tracks, you want to keep on recording on one long track.
There must be lots of software that allows you to edit WAV files. I'm not familiar with you're recording software, but you should have the option to save it as a WAV file. I'd actually be surprised if the software you have doesn't let you edit the track itself. But if you do need some other software, search for "WAV editor" on google.
I'm sure there are plenty of programs out there that will do it. Probably even some free ones. A mate of mine regestered one that was shareware recently for as little as US$10. If you do find a share ware one that works for you, it's always a good idea to send the author some cash. A lot of effort goes into even the simplest programs (I should know, I'm a programmer).
If you're really serious though, get cooledit. It has lot's of extra features. BTW, there is a WAV edit that comes with Nero 6.