I'm not 100% sure which way will give you better results in the long term. I've seen them both used.

Usually I pick the low string 2 times, which means use the former.

The general rule is to always hit the string from the direction you're attacking.

However in the Steve Vai's 30 hour workout there is an exercise where he used the latter, and he only hits the low string once, on the downstroke. It some situations I might use this, but it's uncommon.