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Adding to what Colin and Suavi said, you should pick a single sub as the reference and align all your other subs to it. It doesn't matter whether you do the alignment all at once or in smaller batches so long as you only align to that single reference frame.
You will get best results if you pick the reference carefully and use a good quality sub. Look for a sub with tight, round stars and no obvious guiding problems. The SubframeSelector script in PI can show you a plot of metrics such as FWHM and Eccentricity to help make this choice. It's also worth using the Blink process to check your subs visually.
Cheers,
Rick.
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