Tomlong has some nice instructions on her site. It's linked in her sig and easy to find.
BOSS has complete instructions in the readme for it, but really all you have do is install it correctly, turn off lock times in Wrye Bash, and then click the "BOSS" button in the bottom bar of Wrye Bash.
Bashed patch is created by right-clicking it in WB, and choosing "Rebuild Patch", then just choose the options you want. Some of the overhauls have specific instructions for their own mods. Tomlong has specific and general instructions on the aforementioned website.