When ModBuddy builds your mod, it should place a copy in your MODS folder automatically.
All you need to do is to load Civ5, and click on "Mods" on the main menu, then accept the little warning, and go through your list of mods, clicking the little 'checkmark' circle on the right side of any mod you want to enable. After that, just hit Next > Single Player > Set Up Game > etc. as normal.