"BDmapq" is an integer specifying the minimum mapping quality for a read to be used by the algorithm.

"readsToSample" is also an integer, this time giving the number of read pairs that should be used to estimate the insert size of your library.

However, you can omit both and Breakdancer will use its default values. You can find a few more details of the arguments here: http://breakdancer.sourceforge.net/bam2cfg.html

The "bamfile" argument is a space separated list of the bam files you want included. You say you have at least two bam files per sample, so you probably want something like: /home/myfile1.bam /home/myfile2.bam

The final part, "bd.config", is the name of the config file to be created. if you don't include it the resulting config information will be printed to the screen. Using ">" will direct that to the specified file, rather than the screen.