i had mine done last weekend, and the sections that were welded are accessible in situ but.. i would definately recommend removing the subframe, and stripping it of wishbones and arb to do this.
quite simply the metal skins not actualy that thick, and the heat from the weld travels, as i welded near where the wishbones are mounted, leaving them on would risk melting the bushes

or worse..
re-assmbly is reversal of removal, but i recommend fitting polybushes at the same time

also clean as much of the collected dirt/crap as you can off the subframe, it'll probably save you a few pounds of kerb weight, for a while anyway

ninja