WebKit and Chromium are different repositories, and point to each other via a "DEPS" (dependencies) file. We roll new revisions of WebKit into Chromium regularly, and call the process of diagnosing and fixing problems with the rolls "Gardening": http://www.chromium.org/developers/how-tos/webkit-gardening is a good reference.
You mean having full-time engineers handling merge conflicts / upstream breakage / regressions / running test suites? In anything sufficiently large, that becomes a major issue inevitably.
Almost any project worth its salt has someone doing testing. But it is really time consuming.
