If you use the commissioner's league I'm pretty sure you can. I could have sworn I saw that option last year, but it's not showing up right now. Sometimes in the off season when you haven't yet paid for the following year you don't see everything there is.
We don't allow it in our league, so I don't know how it works if it is there.
But even if the interface didn't do it automatically, you can always manually change the draft order to complete the trade by going to
Setup -> Draft&Rosters, clicking the "set draft order" link, then finally clicking the "Set Customized Draft Order" link on the draft order page. You're able to set picks for each round of your draft there.