2) If in the "value" column where I expect a higher number has a "value of 10" or less mean anything or should one be selecting for values higher that these single digit numbers
3) And in the column of genes that might be repressed is there really a difference between a "value of 0.1 versus something like 0.01" since that can change my log ratios significantly--this, of course, goes back to my first question
These questions get at the challenge of interpreting FPKM values. One thing to look at is the confidence intervals (CI) produced by Cufflinks/diff. CIs that overlap 0 are, in my experience, unreliable no matter how large the FPKM.
Most likely genes with FPKM values near 0 have CIs overlapping 0, which means there's likely no difference between them. However, genes with low FPKM values ( e.g. < 10) but tight CIs and > 0 should probably be included for further analysis.
Another thing to look at is whether a couple highly-expressed genes are reducing FPKM values. If so, using the upper-quartile normalization option can help you get better resolution for genes expressed at low levels.
J.