dep init   

dep ensure -add github.com/foo/bar github.com/baz/quux

dep ensure

dep ensure -update is the preferred way to update dependencies, though it's less effective for projects that don't publish semver releases.
dep ensure -add is usually the easiest way to introduce new dependencies, though it's not the only one. To add more than one at a time, you'll need to use multiple arguments, not multiple invocations - and make sure to add real import statements for the projects after the command completes!
If you ever make a manual change in Gopkg.toml, it's best to run dep ensure to make sure everything's in sync.
dep ensure is almost never the wrong thing to run; if you're not sure what's going on, running it will bring you back to safety ("the nearest lilypad"), or fail informatively.