Victor,

I got the normalized values (FPKM) from cufflinks. And I want to get relative reads counts. How can I do that?

It's not clear to me what you're looking for. FPKM is a normalized read count metric where the F stands for fragment, which is a single read (or half of a paired read).

Another question: how does cufflinks handle isoform genes while calculating the reads counts?  Or what papers can help me understand this?

Expectation maximization is used to probabilistically assign reads to isoforms. See the Cufflinks documentation for details and paper links:

http://cufflinks.cbcb.umd.edu/

Best,
J.