How to watermark while encoding with Handbrake

I have a large video file that i encode in Handbrake to mkv format.
I need to add a text watermark throughout the video.
Is it possible to do this in handbrake itself? Or any other encoders that encodes to mkv and uses same encoding algorithms as Handbrake? Because, the output from Handbrake is really good in terms of quality- file size ratio.

P.S: I tried using the output from Handbrake in VirtualDub and Avidemux, but there is much quality loss due to the re-encoding process. Since i have the source file, i'd like to add the watermark during the first encoding process itself.

Thanks for any inputs. :)