Cuffmerge related query

[ParthavJailwala]

I have a query regarding what samples should be merged using cuffmerge, when you have multiple phenotypes (each with replicates). Lets say my mouse dataset comprises of one set of RNA-seq samples resulting from mutation of gene X, while there is another set resulting from mutation of gene Y. So the samples are:

Samples:
GeneXmutation (3 reps)
GeneYmutation (3 reps)
B6ctrl (3 reps)
MixedCtrl (3 reps)

The cuffdiff comparisons of interest are:

Phenotype A: GeneXmutation (3 reps) vs B6ctrl (3 reps)......[GeneX mutation is on the B6 background]
Phenotype B: GeneYmutation (3 reps) vs MixedCtrl (3 reps)....[GeneY mutation is on the Mixed background]

I have the cufflinks assemblies for each of the 12 samples. My question is: should the cufflinks assemblies (transcripts.gtf) of all the samples above be merged one time using cuffmerge (all 12 samples as above) OR I should be running two cuffmerges: one for Phenotype A comparison and other for Phenotype B comparison? Does one approach over the another make a huge difference?

Thanks