I suppose you can stain over your crackle paint. The effect might be a little strange. The stain won't penetrate, so using a wiping stain won't do much. Most likely it would just cause runs and be very transparent. A gel stain will have more color, but this too will be a little transparent.
Depending on the effect you are after, try using paint thinned or cut with glaze. This could have similar effects as a wood stain, but you will be able to control the transparency. Plus have available an infinite variety of colors.