Underside should be cleaned up, primed and painted to prevent it from rusting. If there is not metal over lapping each other, then there is no need to use a sealer.
Also it should be noted that when you weld patch panels into a body panel, the welding needs to be done in stages to prevent warping of the body panel. Weld a small section, let the metal cool than weld another small section, let it cool and so on.
Mario