The bigger the pot size the better in my opinion. But what is most important is how much light are you using in that 3x3? A good estimate for soil size is one ounce per gallon of soil. So if you have a 600 in there many get around 1 pound off one, but lets say you max it out at 1.5 pounds that would be 24 oz divided by 4 = 6 gallons. And it doesn't hurt to have more soil either, it helps the plants grow even bigger in flower from my experience, especially the sativa dominant ones which is what I like. So I would go with a 7 gallon pot since you have plenty of room. Maybe even 10s , I like big pots. I have tried both the Smart Pots, and the Root Pouches and personally prefer the Root Pouch more and they are a lot cheaper then the Smart Pots on ebay.
And as far as transplanting your clone, I have done it both ways. The results are fairly similar but I think it may be a little better for growth if you put it in another smaller 1-3 gallon pot before the bigger 7 gallon smart pots. I have put them straight from a solo cup into 15 gallon pots before and it wasn't much different. So if you don't have the pots on hand or just don't feel like messing with it then go ahead and put it in the bigger pot. But with having both options, I always put mine in 1-3 gallon pots before transplanting to their final resting place. One last thing, if you plan on going bigger in the future then get bigger pots and don't put a much soil in them. Meaning you could get a 10 gallon pot and leave a 2-3" gap at the top with no soil so that it would only be like 7 gallons. It makes watering a lot easier and gives you room to grow in the future.