Stacking all the individual subs at once will provide maximum information for the rejection algorithm to chew on and should produce the best results. Splitting them up into large batches is going to be nearly as good but I definitely wouldn't do smaller batches, like one each night.
I have been able to stack hundreds of subs at one time with PI on a Windows system with a relatively modest configuration, at least compared to the average gaming computer
On a Mac I think you're limited to a couple of hundred max because of a dumb OS limit on the maximum number of open file descriptors.
Cheers,
Rick.