Maybe you already know but doing paired-end alignment you should do something like this

[prompt]$ bwa aln hg19.fa forward.fastq > forward.sai
[prompt]$ bwa aln hg19.fa reverse.fastq >reverse.sai
[prompt]$ bwa sampe hg19.fa forward.sai reverse.sai forward.fastq reverse.fastq > my_alignment.sam

Where "sampe" stands for sam paired-end.

You might benefit from reading Heng Li's presentation on BWA alignment and look what he has to say about BWA and SNP calling or reading Workflow Or Tutorial For Snp Calling?.

I think you should use the default values for most of the BWA parameters. They are already tested and most of the people use the default values. The maximum edit distance or mismatches allowed in a read is automatically decided depending on the read length. so you may not have to worry about that.