You can do either. I like to combine them for a few reasons... one, smaller amounts of hash are harder to scoop out of the bags. I prefer a larger clump because it’s easier to work with.
Two, one run (compared to several smaller runs) will be more time effective. Each run takes about an hour and each batch needs to be washed at least twice. So run time alone (not including set up/staging time) will be about 2 hours per batch.
Check out my sig. for my bubble hash tutorial.