Richard asked me about the process I use when dealing with the sill area, which I took to mean the conventional sill replacement process, also I don't know we were referring to a freshly e-coated shell. With this in mind, please ignore the above
I have to confess (and don't want to be a party pooper here), I'm not a great fan of dipping and e-coating fundamentally solid cars for all sorts of reasons. Point being for purposes of this particular thread, is that I've never cut out and replaced this area of the car, and wouldn't. Just my own personal view.
If I remember, and it's a while since I've worked on an e-coated car, it's horrible stuff when hot, and gives off loads of fumes, and leaves black streaks etched into the coating, a sure sign of very aggressive fumes. I bet if you deliberately put a bit of clean, fresh steel right next to some e-coated metal, and then welded the coated surface, within a half a day or so, the bare steel sample will be showing significant corrosion. Do the same welding perfectly clean steel, and you'll have no problems. Might be wrong, happy to be corrected.
Therefore I'd imagine you'd need to clean back by a good 1/2 - 3/4 inch on both sides of the proposed weld site, prime back up with the Wurth Zinc Hell or similar, I.e. anything that is a genuine weld-thru primer: beware many claim to be, but often this just means it'll more or less burn away given enough heat. Best way of telling is by painting a surface and trying to MIG weld a bit, and then try spot welding it. If both welds perform the same as no coating, it's a genuine weld-thru. If the welds are compromised, it's not a weld-thru primer in my eyes.
That's many feet of really hard cleaning I know, but probably the only way of getting a really nice sounding and looking weld.
As for the etch priming, well clearly it's e-coated, so you're not gaining anything by adding a primer over that in cavities, and a good cavity wax later on, refreshed every five years or so should keep it all good.
Sorry to sound a bit down on the process, and I wouldn't have chipped in had my advice not been posted (which was absolutely fine, just a little out of context in this case).
Best wishes for now

