In my experiments with Onion skin it seemed to take a lot of onions, started with a 5# bag and went from there. Never got a color I was happy with, maybe I did it wrong. Would like to hear amounts and procedure. I have tried the process in Sibley's Recreating The 18th Century Powder Horn but still did not get what I was looking for, His explanation on the use of Dye gives exultant results, as does the use of Aquafortis. Kind of depends on what you are looking for or trying to reproduce.
You can put a horn with base in a pot of liquid but you will have to put a weight on it to hold it down, filling the horn with liquid helps. Also the spot where the weight touches the horn may not color as well as the rest of it. You also run thee risk of the wood expanding and cracking the horn.
To answer the above question, for me anyway, putting the base in is the last thing I do, I find it hard to hold/work on with the base in. If there is any touch up to do to the color it is easily done. If I did carve horns I would carve, color the carving then age the horn, kind of the natural procedure.
To each his own.
Tim C.