Tuxedo cannot handle technical replicates. If I were you, I'd consider the following route:

Gene Level: Align with your favourite aligner -> count using htSeq_Count or rSubRead -> Use DESeq2 for Differential Gene Expression. (read about technical replicates here in section 1.3.7 and how to collapse them).

Transcript Level: Transcriptome quantification using Salmon (read about making Salmon counts friendly for Sleuth here) or Kallisto -> Differential Transcript Expression using Sluth (I haven't used technical replicates here, so you may have to do some reading, but it's by far the best way to do differential transcript expression)

edit: To answer your original question, your way of accounting for technical replicates seems right, however I'd consider feeding your cxb files from cuffQuant, into CuffDiff.

edit edit: If you're looking for a more flexible way to model your experiment, besides pairwise differential expression, then the routes I explained above are your best shot.