As long as you properly labeled the box you sent in for the signing, it should be pulled and set aside for the designated in house signing.
That being said, CGC has recently changed their magazine holders to be more like the current CGC comic size cases, so I wouldn't be surprised if you don't have a year+ long backlog of other magazines ahead of you when your magazines hit grading. For example, I submitted some magazines to an in-house signing last May, and they're still in "Grading / Encapsulation / Imaging". Your milage may vary, and by the time the signing happens, the backlog could be severely reduced.