Hi, thanks for checking the game out!
If you're using notecards (as opposed to the worksheet), you'll only add notecards to the journal once you create the suspects, so you shouldn't have any blank ones in there for the killer to be bouncing around in.
If you're playing in worksheet mode (which is much less developed at this stage), I've done it both ways. Usually I will just pretend like the blank squares aren't real and keep the killer in the populated section of the journal. But there was one moment in a solo playtest where I used that situation as an opportunity to add new suspects and spice up my story.