Looks like you actually already have the right code in place to make this all work, you just dont know what you've got. That probably means you copied code/structure from someone else. That's not a horrible thing, that's how we all learn.
You just need to think about this a little different.
First, try this for your "start" function. Lets call it "pause" instead.
Func _pause()
if $active = 0 then $active = 1
elseif $active = 1 then $active=0
endif
EndFunc
This turns pause on and off, letting you pause and unpause the program anytime.
Next, your main routine needs to reflect that. Lets add a waiting while loop
While 1
while active <> 1
sleep(500)
wEnd
If $active = 1 Then
MouseClick ("left")
MouseClick ("right")
active = 0
EndIf
WEnd
So, this checks to see if you want the program active. If not, it waits 500ms, then checks again. As long as active=0, it just keeps checking
If however you press unpause (active) it runs your "if" once, then turns active off again, and it goes back to checking.
Does that help?