I just figured out how to put a small amount of dip and dye on my plastic baits, without dunking them and going too deep.
I shake the plastic bottle, set it down, take the top off the bottle and lay it next to the open bottle. Then I take the claws, or swimbait tail, that I want to dye, and push it into the cap. There's enough dye left from me shaking the bottle to dye one bait, and that way I have more control over where the dye goes.
I use the pens as well, and actually prefer to use them, but I carry a bottle, too, because the pens dry out sometimes.
Just something that works for me.
Do not try it on a windy day, or in rough water, unless you have a dye-proof area in your boat to do your dye work. Otherwise you will wind up with chartreuse carpet, sooner or later.