Unfortunately I know exactly how you feel. I had the same issues with a receptionist - who was the friend of the Presidents pet at the time - so after I complained about her and he refused to believe me (a 5 year employee over someone that had been there for a few weeks) I told him under no uncertain terms would I be responsible for her if he wasn't going to allow me to manage her as I saw fit. He said fine....things steamrolled from there and I quit about a month later - while she sat at the desk with a cat that just ate the canary's grin on her face.
Well after I left all these bad things kept "mysteriously" happening until she was caught in so many bold faced lies and untruths it was obvious to Stevie Wonder that she was the miscreant in the office. There was not enough money in the world for me to even consider taking that job again but her mistakes cost him a grip of money and offended a number of donors who never returned. To say I laughed when I found out what happened is an understatement and it took everything in me not to call and say I told you so.
So that is to say I don't know why your boss is taking a liking to her to the point where YOU the person that she is to report to is not allowed to do your own job (which is namely to manage her). Talk to your boss - not putting blame - just ask - why is the secretary meeting directly with him? That is putting you in an awkward position and is creating a communication issue (as in the chain of command).
As far as seeing if she is there why not call the office - if she doesn't pick up you can summise that she left early (that's how we caught another liar - she was suppossed to come in at 8:30 to set up and was actually coming in at 8:55 every day until the cleaning staff ratted her out
).