Need help...'98 golf GTI both rocker panels look like swiss cheese under mldgs. Any advice or suggestions?

Sorry I dont have any helpful info. If the rocker panels are rusted out, you should check on the condition of other stuff under the car; brake lines, underbody structural sections, the attach point for the suspension, the condition of the walls of the 4 strut towers, the floor under the carpets...
If the rust is really only on the rocker panels, you could have a body shop just slice out as much rotted out surface sheet metal as they can, and rivet new sheet metal over it. This wont make it look new - but at least you wont get cut on the jagged edges. (In some states, a hole rusted through has to be fixed/covered/puttied shut; even if its looks crummy).
If the rest of the bottom of the car is as rusty as the rocker panels - the only thing I can recommend would be finding a similar car that spent it life in Texas or Arizona - and use your car for parts.

Had the car at friends body shop...took off rocker moldings(salt-dirt catchers) and top mldg with metal insert is rusted also. This car is clean-non rusty any other place. With the mldg on, you can't even see rocker panels. I was thinking of cutting out rust, patch, then body seal repairs with new mldg panels.