Variant calling with multiple individuals and libraries.

I have multiple individuals. Let's say they are S1 (Subject 1), S2 and S3.
There are two Chip-seq libraries for each subject (AC, ME).
So I have 6 libraries in total. S1_AC, S1_ME, S2_AC, S2_ME, S3_AC, S3_ME .
I want to perform variant calling for these subjects. I have run the alignment, indel realignment, calibration for each of the 6 individual libraries and now the bam files are ready for variant calling. Now, how should I run variant calling? Should I merge the bam files for each individuals like:
S1_AC S1_ME > S1
...
and run variant calling for each individual?
Or should I process each library separately? If I put the sample name the subject name to each library of that subject using AddReadGroups (RGSM=SX), does HaplotypeCaller understand that they come from the same subject?
I will really appreciate if you can help.