I'm having a little trouble understanding exactly what the problem is. However, Stencyl supports 32 sound channels. Each channel can have it's own volume / fade in and out, etc.
Which platform are you developing for? Flash? As far as I am aware, there are no problems with channel management on the Flash platform.
Are you specifying the soundtrack as 'music' and the effects as 'sound-effects' when you are importing the audio files into Stencyl?