Individually. You want to start with the original quality, not with compressed, encoded and compromised material.
From Premiere, use File > Export > Media to open Adobe Media Encoder. This will encode to whatever output format you want, from the original source clips in your project. You can actually set up multiple exports to different formats and sizes using the "Queue" and then render them all at once.
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Either way works, so long as the Master you create is of sufficient quality.