Well, it seems an old question, just may be help to other people :) It won't make sense if you merge the point clouds without registration. Thus ICP should be employed. Then you can perform transformation to the corresponding Point Cloud, and merge them after that. Should be straight forward.
The only way that I have been able to figure out how to concatenate clouds of two different sizes is to pad the smaller cloud up to the same size as the larger cloud. I did it by testing which is largest then filling a temporary cloud with the smaller cloud and then filling the balance with 0 0 0.
The other way that I see is to create a temporary cloud with all 0 0 0 points and then filling the lower portion of the temporary cloud with the smaller cloud.
I think the latter is easier to implement but the former is faster. I used the former.
http://pointclouds.org/documentation/tutorials/concatenate_clouds.php#concatenate-clouds