problem with recording seperate audio tracks

It’s difficult to understand your specific issue. May be it’s just you don’t realize media players will play back only one track at the time. Either they play back track 1, or you switch in the media player to track 2, then it’s playing back track 2. Media players will not mix audio tracks and play back both at the same time. To make use of multi track recording, you need to postprocess the 2 tracks, mix them in a 3rd party tool, then replace the 2 tracks with the mixed track.