Will I still get direct deposit after amending my tax return?

I filed my taxes and they were accepted. A couple days later, I got a W-2 for a job I worked a couple weeks into 2016 and forgot about. I came to TT to create an amended return so I could print it and mail it in after I got my refund, since I knew the W-2 would generate a little more refund, instead of me owing money. 

My problem is that now, my return says I will be receiving a paper check I am assuming due to the amendment. However, I cannot e-file an amended return so everything the IRS received has not changed. 

My question is to see how I can be sure that I will receive the refund in direct deposit? I know the IRS has my direct deposit info, BUT I gave TT permission to deduct my filing fee from my refund, which means they will get it first. How can I be assured that the refund from my original filing will not take 20 weeks to get to me?