Should I be using UserInputService instead of MouseButton1Down?

That really depends on what you're trying to do. I recommend using MouseButton1Click, MouseButton2Click, MouseButton1Up, MouseButton1Down, MouseButton2Up and even MouseButton2Down when using a single, simple function, for example, changing a team color, tweening a gui's size or position, changing texts, destroying and cloning things...

But UIS (UserInputService) should be used when making more complicated functions, and SPECIALLY when using keys on the keyboard.

Here, the first option (of the MouseButton1Click, etc.) should only be used when you're making a function with the MOUSE, and more basic functions. But, if you're trying to make functions with KEYS of the keyboard, which are normally more complex, I suggest you totally to, instead, use UIS.

EXAMPLES:

Using MouseButton1Click:

script.Parent.MouseButton1Click:connect(function() --script.Parent is a TextButton
    script.Parent.Text = "The button was pressed now."
end)

When using UIS:

function onKeyPress(inputObject, gameProcessedEvent) --if key is pressed
    if inputObject.KeyCode == Enum.KeyCode.R then --if "R" key is pressed
        print("R was pressed") --Code, which is the example **print "R was pressed".**
    end
end

game:GetService("UserInputService").InputBegan:connect(onKeyPress) --Get UIS and check if player inputs any key (on the keyboard)

EDIT

If you want the UIS and pressing A on the console, simply set a function and then call it, like this:

function click()
print("CODE GOES HERE!")
end

function onKeyPress(inputObject, gameProcessedEvent) --if key is pressed
    if inputObject.KeyCode == Enum.KeyCode.R then --if "R" key is pressed
        click() --Call click() function, which was set there up.
    end
end

game:GetService("UserInputService").InputBegan:connect(onKeyPress) --Get UIS and check if player inputs any key (on the keyboard)

--And here you should put the "Clicking on A" function on the console... and then call the click() function, like how I did there up.

Hope I could help, and if you found this useful, please mark as the solution!

As always, keep the good scripting! :P