Three questions:

1)Maker = Beyonder?

2)The Living Tribunal > Beyonder/Maker right?

3)???>The Living Tribunal/Beyonder/Maker

Maker = Beyonder (till there's a retcon)

Living Tribunal is not nor is in any known way related to the Beyonder/Maker.
Originally, The Beyonder was considered more powerfull then the Tri-Judge and most all of the powers of the Marvel Universe (as seen in Secret Wars 2, issue #6), but, that's been retconned, and in a bad way. (I blame John Byrne, whose on record for hating Jim Shooter, who created the Beyonder).

And The Beyonder has been retconned yet again recently in "The Illuminati" mini that came out not to long ago.

Try wikipedia for more info and more of his other names and associates.

http://en.wikipedia.org/wiki/The_Beyonder

That should help a bit.

Nothing major seems to happen unless the Living Tribunal is cool with it, so I think the Living Tribunal right is probably Joe Queseda. Considering all the shenanigans he's been up to, I don't think anyone is strong enough to stop him right now. Maybe someone will retcon that though.

Well, they did retcon away most everything Jim Shooter had done, so, why not?
Actually, the company that owns Marvel could thwart Joe Q. Then, when you think about it, it has been stated by the Tri-Judge himself that there is a power above his own. The one he recieves orders from. I think he calls him "The One Above All". I'd equate that with the owner(s) of the Marvel company.