You can use [?]Samtools[?] (http://samtools.sourceforge.net/) or [?]Picard tools[?] (http://picard.sourceforge.net/command-line-overview.shtml) to merge your bam files into one single bam. There should be no problem in merging two bam files of differing read lengths.

Assuming the bams are already sorted. it's as easy as:

samtools merge combined.bam 1.bam 2.bam

The read lengths don't matter from the perspective of a bam file. They might, however, matter to some of the algorithms you wish to apply. You should be aware of that possibility.