Why wont the lines inside this if statement work?

Because Touched is an Event, it does not return a boolean, you should connect a function to touched instead

clickDetector.MouseClick:Connect(function()
    local clicked = true
    humanoid.WalkToPoint = workspace.gen1.toolbox.walkto.Position
    if clicked == true then
        workspace.gen1.toolbox.walkto.Touched:Connect(function()
            humanoid.WalkSpeed = 0
            humanoid.JumpPower = 0
            local animTrack = humanoid:LoadAnimation(animation)
            animTrack:Play()
        end)
    end
end)

And also your Clicked Boolean is redundant, as the Touched event will only ever be triggered when you Click the ClickDetector. So there really isnt a need to check for "Clicked" unless you are doing it for debouncing