I've made 2 tone swirls before by lining half my piping bag with one color, and half with the other color, but when I do my swirls, they always seem to come out with one color on the left half of the cupcake and the other color on the right. Does that make sense? The icing is coming out 2 tone, but they way it's falling on the cupcake is each color directly on top of eachother, so the cupcake looks half and half. What I'd really like to achieve and what I've seen before is where the outer edge of the swirl is one color and the inner groove of the swirl is another color. So the "tips" of edges of the icing are a different color than the rest. Does that make sense?

Use bag striping with gel colours

http://www.wilton.com/decorating/icing/coloring-icing.cfm

or with frosting?

http://www.courtneyssweets.com/2009/04/somewhere-over-rainbow.html

BTW, I love the rainbow cupcakes in the 2nd link.

HTH,
Debbie

aside from the painting or spatula method, you could also use frosting plugs (try seriouscakes on youtube for a tutorial on frosting plugs) or you could pipe a stripe in your bag with another piping bag (make sense?)
with regards to the same colours landing on top of one another I guess that depends on what tip you are using and what type of swirl you are doing, not sure how you'd fix it tho, sorry, that wasn't much help at all was it!

Just thinking how to do this and wondered if you could use the two colors but make 4 alternating sections of frosting in your bag. Do you think that would do it? I'm trying to imagine the swirl that it would make. You might get a better distribution of the two colors that way. Maybe?

You have to line the bag then fill with the plain color buttercream. Like my rainbow cupcakes above and my memorial cupcakes..
http://www.courtneyssweets.com/2009/05/happy-memorial-day-god-bless-america.html

I took a wooden dowel and put streaks in the bag. Say if you do chocolate stripe the bag with the chocolate then fill with the regular white. KWIM?..