Cheetoh- Actually, 3M's SMR is designed for EXACTLY that purpose, the removal of very minor, rotary induced swirls. It's OK to use a (preferably mild) abrasive polish on new paint, most likely the shop already did (and they caused your swirls in the process).
*BUT*, as Deanski said, your REALLY oughta take it back to the shop. They botched up when the gave you the car with marring in the finish. Let THEM fix it, then it's ALL on them. Otherwise they can blame YOU, say you caused it. Make sure they don't just glaze it with something containing a lot of fillers (this includes 3M's SMR) or the problem will just come back. You paid for it, make 'em do it right :xyxthumbs