I understand where you're going with this, but I woulnd't use the pen to make a new color on your vinyl. Actually, I'm not even sure how you would make a "fill" with your pen without hundreds of individual lines...
Anyway, if you're talking about regular stickers, what you could do is buy a good printer and a plotter with an automatic registration mark sensor (ARMS) and print your stickers, then contour cut around them wiht your plotter.
If you mean vinyl for t-shirts, you would just make your design vinyl-ready, then for each color in your design you would cut a new color of vinyl, then line them up individually on your shirt.
Basically the same for sign vinyl. You'd cut each color seperately, then line them up on your substrate.
There are three plotters that I would recommend...The Graphtec CE5000-40 CraftROBO Pro for t-shirts and regular stickers only...The Graphtec CE5000-60 24" plotter for t-shirts, stickers, and signs (we have this plotter and LOVE it!)...and finally, the most common plotter here on these forums (tho a little more expensive), The Roland GX-24.
Price-wise, the Graphtec is the best VALUE, but I suggest reading all the posts you can in this section to decide which one you'd like to get.
All three of those plotters are available at
Specialty Graphics Supply
BTW, if you would like to pen-plot on paper, the Graphtecs are the only plotters listed above that come with a pen...
Good luck!
making stickers plotter pen holder 
