Hello
You need to run only one big 3dDeconvolve modelling all the trials individually, i.e. the 32*2*6 in one single model. However, you could also run 3dDeconvolve and 3dLSS for each individual run since 3dDeconvolve is only used to create the design matrix for 3dLSS. Of course, 3dLSS will have to be run for each run separately too.
Hope this helps,
Cesar