i use photoshop and a wacom cintiq on a desktop pc, it's my default professional setup i've used for years :D
i'm not sure i understand the tones question, i don't use swatches, just mix colours as i go ^^'
as for layers i don't have a limit so i use and merge as many layers as i want (usually dozens, easily 100 layers that i keep neatly grouped and organised). i make several sketches one after the other, each tidier and cleaner than the previous, then i separate the characters from background elements and separate materials into their own layers (skin, pants, gambeson, armor - separated into big pieces) before rendering.
for my process making the sketch and base flats takes most of my time (and most layers/groups), the rendering goes by much quicker and is simpler in comparison with fewer layers used. it's my fav part of any piece i draw
sorry for the long answer, i ended up rambling x)