Your board's manual should tell you how your channels are split..either 1,3 2,4 or 1,2 and 3,4. As long as you put the pairs in the same channel, it shouldn't matter.
You should be okay with installing all of it first, and then installing Windows 7. Vista had some issues with certain chipsets, usually Nvidia, where it didn't like seeing a lot of memory for the install, but was fine if it was added later. Those issues have been scarce and aren't much of a worry anymore. However, if you decide not to chance it, I'd put in the 8 GB alone, and then install.