Timer and input

As I'm making a program that does test, I have it run both time and waiting for an answer using multi threading, but the problem i have is that timer always put the console cursor at the location of the timer, thus waiting for the answer there... which pisses me off.
Is there any way to make the program to write down the timer outputs without moving the cursor to the position?
If you need I will post some part of the code.
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So, any ideas?
I could do it in Qt, but I'm not sure about the console.

In Qt, I'd just link the stdin to an editbox and make a Qtimer function update a static text widget.
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