You can't do it quick and dirty, in that case. The colors are being selected in two different files when you do it that way, and you won't be building on top of the higher level (theme) file when you move the lower level (user) customizations into a separate theme file. You can only have one theme file at a time.

What you could do is write down all of the hex colors that you selected doing it your way, and then go back and do it this way, writing in all of the hex colors on a clean slate, and then proceed from there.