Audacity is a linear audio editor and you sound like you were trying to use it as a non-linear DAW, which feature bloat and undo/redo sort of but not really lets you do. A media manager does not really help in this sort of editor, your timeline is not an arrangement of files as it is in a daw but the actual audio file you are arranging and changes are destructive. Linear editing is like working with tape, your changes are permanent, every change alters the medium (the destination audiofile held in memory in this case); non-linear is like a sampler on steroids and is how DAWs function, you arrange the samples (files) in time and then record them out to a file when things are how you want it.