If your 100% sure that the rest of the rail is fine then definately just patch that section.
I went for the caps because:
A) I'm in Australia and I can't check the papers to see whose wrecking an E Body
B) Whenever I'd patch one section, a crack would appear somewhere else!
C) The caps, even with their ugly welds look better than my squashed, dented and rusted rails!
D) I plan to drive this car hard, so the re-inforcing will be a good thing.
Unless your in a similar situation, avoid the caps. They're not a bad thing, just overkill if you don't need them. And lots of work.
I'll post some photos once I get them fitted.