The first thing that has to be mentioned is that you do not want to be running UNISOUND from within Windows. UNISOUND is a complete, stand-alone initialisation and configuration tool for DOS, and there is always some risk of completely pulling the rug out from under the Windows configuration manager and Plug and Play sub-systems. In specific circumstances, this can lead to bad things happening. Even absent those particular situations, it is generally not a good idea.
From the behaviour you're describing, it sounds like the DOS title you're trying to run is using Sound Blaster compatibility mode, correct? If that is the case, it is a side-effect of the way Crystal implemented the mode switch. In switching to compatibility mode (from the native WSS mode used by the Windows drivers), default hardware values are used for the Sound Blaster Pro mixer; the default for the line input is 0 (mute). The safe way to get around this problem is to use a DOS tool that will set the SB mixer values only (no other initialisation performed). Obvious choices are CWDMIX or the original Creative SB Pro mixer tool.
It is worth pointing out that, for this to work, you will have to open a command prompt, use the mixer tool, and launch your DOS title from that same command prompt. The second your DOS session ends, the Windows drivers assume control and restore the WSS state, causing your changes to be lost. Another option is to create a batch file that first applies your SB mixer settings, then immediately launches the DOS title you want.