I used Format Factory by Formatoz, for this work.
There are several other softwares available, but I am used to it.
Now, the steps involved are as follows. First of all, open the Format Factory window (after installing it, of course). The window will be similar to
Then, click on the videos section at the left, and chose the format of the video, which you want for your final result. You will now get a window like this:
Click on the Output Settings button there, and chose any one of the media type from the list
There, in the Output Settings window, you will notice The watermark written there. Expand it, and it will look similar to
Click on the ... written in the first line of watermark category. This will then look like
After clicking, you will be asked to chose a file as shown,
Select the file you want to add as watermark, and click OK in the Output Settings window. There, you will have to addd the file / folder to add files which you want to watermark. Select them like this one:
After all the above steps, just click on OK again, and click on the Start button located on the top. The work will be completed later, and you'll be notified about it.