Like they said, you need to take them both off. Don't separate them unless you have to. Whenever I replace the manifold gaskets on the six, here's what I do to help stop the exhaust leaks.
First, clean the mating surfaces. Sand down any rust, remove the old gasket material, and finish the cleaning with a good solvent, I prefer lacquer thinner.
When ready to re-assemble, I put a coat of Permatex Ultra-Copper RTV on the manifold surfaces, then put it all back on. I have used the knock-off rtv, but the Permatex sticks better.
