Questions: Cufflinks FPKM

[lewewoo]

After cufflinks and cuffcompare, every transcripts were assigned their FPKM numbers, some papers used the longest transcripts to present the gene FPKM, others used the transcript with highest FPKM to present the gene FPKM; my first question is which one is better if comparing expression differentiation.
I also used CuffDiff, there are FPKM tracking files, and it is said that the FPKM for expression comparison is a sum of all the trascript FPKM, is this way better than those as above?
Thanks!