Yes. You can either make it free or fill in the amount you want to charge for shipping. The buyer only sees the total price so I don't know if it really makes a difference which way you do it. For lower priced items, I figure if I can cut out some of the shipping price, I can charge a little more for the item. You should realize that Tradesy will take their commission out of the entire amount, so if you are using a flat rate envelope which is about $6.45 now (but that price might be going up mid January) and you add that price to your item, Tradesy will take about a dollar out it. I figure I'm paying more to Tradesy so the actual savings is only about a dollar.
I tend to only use my own shipping when I can ship first class. I ship scarves and keychains first class. Clothing is often too heavy, but not always. I can ship up to 8 ounces for $2.60, and up to a pound is around $3.60. That makes a big difference in the price I can charge. With first class, you don't get automatic insurance.
Also, if you use your own postage, I believe you are responsible for the package until it is delivered, whereas once the Tradesy label is scanned, they are responsible.