1. When we are uploading data, one of the fields to be populated is "Genome". Why or where is galaxy using the genome information during file upload?

Genome data is not used during upload but is often used subsequently. Because it's often an important piece of metadata, Galaxy encourages users to set it immediately on upload.

2. During Cuffcompare analysis, we can provide 3 files, two GTF files output from cufflinks and a reference annotation file. When cuffcompare how does it use the annotation file?

This question is best addressed by reading the Cuffcompare documentation:

http://cufflinks.cbcb.umd.edu/manual.html#cuffcompare

3. If cuffcompare is run using one cufflink GTF file and one reference annotation file, what are we supposed to do during cuffdiff analysis where you have to provide 2 sam/bam files?

Cuffdiff is only appropriate for comparing RNA-seq samples. More information can be found in the cuffdiff docuementation:

http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff

Is there any documentation/manual (except for what is on the UI) around that can help answers these (and some other basic questions I have).