‘Bottom-up’ or ‘top-down’ doesn't refer to the question whether the boss has designed the project or the employees or beneficiaries/clients (see Participatory design).
Instead it's about the choice of designing the intervention logic by starting with the activities or with the main purpose of your project:
Whatever way you prefer, you can do it in Logframer. When you list the activities first, Logframer will create a place-holder output and purpose