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You will get different results from one big stack vs several smaller stacks due to the data rejection algorithm (just stacking without data rejection would give you the same result).
I'd definitely do one big stack in PixInsight. Experimenting with different rejection algorithms and comparing noise stats can make a significant difference to the result. Some algorithms tend to do better or worse depending on the number of subs. My experience is that the more data you have the better you can tune the algorithm and rejection parameters.
From memory, CCDStack doesn't give you as many options but I'd expect that you'd still get better results with more data. Perhaps you should try both strategies and see if you can notice a difference...
Cheers,
Rick.
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