[humanpuff69]

I have not yet used handbrake, does it has video and audio mixing option?
Which software is best for adding animations to the video?
I used FFMPEF and mencoder for conversion.

it have that feature . handbrake is more efficient but it support less output only mkv and mp4 whereas ffmpeg have more format support
for adding animation you need more than just video converter

[Kururin]

Handbrake has everything you need, just consult youtube if you are unsure of something, it has great videos on how to do encoding on Hanbrake and other muxings's options.