I also used Scottrade along with Ameritrade. When I sold my positions I had with Sccottrade, I closed my account and went all in with Ameritrade. If you take money out of Scottrade be sure to have them send you a check as it takes forever to transfer funds from one broker to another.
You can merely transfer all of your stocks in the Scottrade to the Ameritrade account. I know I transferred some a while back. There should be forms on their website or call and talk to a broker. They should help you in anyway, they can.