I have just started to do the swirling in the pot. I wait until trace then take out a small portion of the soap I am going to color, add my color, then pour it back into the pot..... I really like this way better than just pouring the alternate color on the uncolored. Because to me, I get a better swirl.... That is just my personal opinion though.
There are two methods that you can use. You can swirl in the mold or in the pot. In the pot is what Earth is talking about. You separate, like she said, color your base (if you desire) and color your swirling soap. for a 4.5 pound batch I take about 3 ladels worth of soap out to color for swirling. When your color is incorporated into your soap, you take your swirling soap and pour it into the pot from various heights. Once you do that, you stir around the pot only ONE time (trust me .. if you stir more than once it kind of gets like a muddy looking mess). You then pour into your mold.
You can also swirl in the mold. Same idea; separate out your swirling soap. Then you pour in almost an S shape, from top to bottom along the whole length (or width, whatever you pick) of the mold. Then, you can use a chopstick, toothpick, butter knife, etc and you physically swirl it like you would a marbled cake.
I like both methods, they do however produce different effects. I found that in the pot swirling produces a softer, more marbly swirlm IMHO. Swirling in the mold produces a more bold and chunky type swirl. It just depends on what you like, as with everything in soapmaking