Pressing and holding the "Space" button will cause you to go up and down. "Z" will cause you to descend rapidy, though you may need the Flight Control Module to do this. You can modify how fast you rise by changing the thrust setting in your Tinker Table, although increasing your thrust will accordingly increase your MJ expenditure.
The Glider seems to be disabled while this mod is in use. Additionally, while the jetpack is enabled, you will move forward at a rate of speed determined by your thrust, and not your running speed. Therefore, it may be useful to bind the Jetpack to a key (press "K" by default to open your binding map), and disable the mod unless you wish to use it.
While it may seem that you descend while moving forward, you are actually simply moving in the direction that your cursor is looking. While you cannot gain altitude by looking up, you can avoid losing altitude by looking straight ahead while flying.