I do all that (well, similar enough stuff). I just have virtual-desktop-per-app (or pair of apps and switch between them <super>+1/2/3/4/5/6/7/8 for left-side

I do all that (well, similar enough stuff). I just have virtual-desktop-per-app (or pair of apps and switch between them <super>+1/2/3/4/5/6/7/8 for left-side windows, <super>+F1/2/3/4/5/6/7/8 for right side. + sometimes a floating terminal window. I3 allows to bind window to "scratchpad" which is basically overlay windows that can be shown/hidden with one key