:qiime2:
Awesome, thanks for confirming!
Woohoo! 
No need to merge! Just import the feature table and then run your taxa barplot command (assuming that the feature IDs match between these two files - they should if they came from the same analysis). Taxonomic analysis doesn't need the observation counts provided by the feature table, which is why you were able to do this taxonomic analysis already with just your rep seqs. You need the feature counts to compute relative abundance and then plot the taxonomic classifications with respect to those abundances.
Keep us posted! :qiime2: 