Combining data sets can be tricky, depending on how you want to process your data. Basically, you want to merge your data set, without merging different samples and different OTUs!
There are lots of ways to demultiplex with qiime, but all of them end up with a seq.fna file with valid qiime labels. This file will be the input to OTU picking. If you have multiple seqs.fna files from different data sets, and all sample names are unique, you can simply concatenate all these files together using the linux cat command:
cat project1/seqs.fna project2/seqs.fna project3/seqs.fna > projects123_seqs.fna
If two samples from different projects have the same name, they will be combined! In order to avoid that, repeat demultiplexing using unique names.
The benefit of combining your data before OTU picking is that you can use any algorithm you want. If you want to combine your data after OTU picking, you must use closed-ref OTU picking. If you don't, the de novo OTUs made from each data set will not match. Using closed-ref picking will avoid this problem because all OTUs will match your database.
Closed-ref OTU picking would solve this problem. :-)
Once you have closed-ref OTU tables, merging them is easy:
Like before, if two samples have the same name, they will be merged. So you may have to repeat closed-ref picking using unique names.
I hope that helps,