From the rulebook:
Instead of eating the Meeples in your Neighborhood, you can eat the Meeples currently
on the Runaway board. Then reorganize the Meeples on the Runaway board without
triggering any effects.
For Side A:
It isn't particularly clear but I think the key phrase is "Then reorganize the Meeples on the Runaway board without triggering any effects." That heavily implies that you should follow the normal placement rules (and are safe from re-triggering previously triggered negative effects). The normal placement rules are:
Place the Meeples on the Runaway board, starting with the top
So I would say that yes, you should "fill the first row and put the remaining 3 meeples in the second row".
For Side B:
It shouldn't matter as they are organised by colour and so the only consequence is a completed track may now be open to be re-triggered in future turns.
Manuals in French, English and German are available at the manufacturer's site.