in my opinion, the simplest method is decoding two compressed video sequences  into YUV format  ,and then combine the two raw video sequences together by one of YUV softwares. Finally, use JM to compress the raw video sequence to the 264 stream. 

thank you zhenkun for your help. do you know any specific YUV software that is capable of combining two video sequences?

Matlab is the best for this purpose

I wrote the the following code that will read odd and even frames from two different video files and store them for you in a new video files.

fileinfo1 = aviinfo('oddframes.avi');

fileinfo2 = aviinfo('evenframes.avi');

fout='combinedvideo.avi';

nframes = fileinfo1.NumFrames;

aviobj1 = avifile(fout, 'compression', 'none', 'fps',fileinfo.FramesPerSecond);

for i = 2: 2: nframes

mov_in1 = aviread('oddframesi.avi',i-1);

mov_in2 = aviread('evenframes.avi',i);

aviobj1 = addframe(aviobj1,mov_in1);

aviobj1 = addframe(aviobj1,mov_in2);

end;

aviobj1 = close(aviobj1);

thank you Nijad for your answer. I'm dealing with YUV video files and unfortunately Matlab does not read YUV files directly, but your code was very helpful and gave me a very good understanding about the whole process and what I need to do. I managed to find a toolbox for reading YUV files into Matlab and with combining it with your code problem solved! I really appreciate your help guys.

http://www.mathworks.com/matlabcentral/fileexchange/36417-yuv-files-reading-and-converting