Maybe apply the light stain 'normally' first and let that dry. Next, apply the darker stain onto a hard surface like a sheet of thick leather and sort of burnish on the darker stain.
Paper towels or cloth materials wouldn't allow you contact just the surface.
Beware of spontaneous combustion if using petroleum based stains. Be careful how and where you store stain soaked materials.
One other thought.... And still using a heavy (thick) leather applicator, it using a wipe on or gel type stain for the darker color. I am thinking leather the thickness of a heavy men's belt. The leather is smooth one side and a bit more rough on the back side. I'm talking raw leather, not a belt. Load the leather with stain by forcing it in using a drywall spreader..... Or maybe a lightly loaded paint brush.
Embed the leather with stain, but not so it's real thick or dripping wet. Wipe it on, or should I say rub it on to the wood, then let it set for a few minutes then gently wipe it off gently with a non fuzzy cloth..
Probably not terrycloth? I'm guessing.
If this helps or not, let us know what you find out.