from an mot and structural point of view, it doesn't matter as long as it's a continuous seam.

inside is easiest, but then you will leave a gap between panels on the underside that will be prone to holding water and rusting again. but you can paint it or underseal or whatever (depending on how much you love your car and how long you want it to last).

if you do it from underneath, then you will have the gap inside, which can be just as bad if you have a carpet that can trap water under it.

you could also do both sides.