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Guys, if I have a recipie that calls for 3 different hops, 60, 20 and 0 min boil. Lets say these hops are Cluster (60min), Amarillo (20min), and Cascade (flameout). If the recipie has cluster at 7%AA, Amarillo at 5%AA, and Cascade at 3%AA, but the AA is lower on the hops I have due to a different batch. Now obviously I would up the bittering hops accordingly, but what about the second two additions, does less AA mean less flavour and aroma or is AA not related to this. I know AA is the bittering agent in hops, and from what I can remember It's the Beta acid that has the flavour and aroma, If AA comes down does Beta follow it down

I'm not exactly sure about this one, but i can clear a few things up.

Alpha-Acids and Beta-Acids are both bittering compounds found in the Lupulin Gland of a hop cone. The reason Beta-Acids are largely ignored in brewing is because they aren't nearly as soluble in water as Alpha Acids. unlike their brother, Alpha Acids Isomerise in boiling water and become very soluble, dissolving into the wort and imparting bitterness.

hop flavour and aroma compounds are found in the essential oils of the hop. these are the volatile oils that are very easily vaporised (which is why when you crunch some hops, the aroma hits you in the face). knowing this is important in understanding why late-hop additions contribute more flavour to your beer and early additions leave almost no trace of the aromatic oils in the beer.

although there is a way to measure the amount of the aromatic oils in a hop (which i don't know enough about to go into), it would take a lot of time and equipment. the best way to tell how much flavour is in a hop is to crunch it and give it a good sniff, or make a hop-tea.

As for your actual question. I have no idea how AA quantities relate to essential oil quantities in a hop cone, if at all. I would assume that a crop with a lower yield of AA would also yield lower essential oils, but I don't base this on any real-world knowledge. In fact, a harsh season might produce an oilier, smellier hop.

I would read Jamil's article on Late Hop additions for an interesting way to get lots of flavour and aroma.
http://www.mrmalty.com/late_hopping.htm

And I found this site very informative when researching this awhile ago. (in fact, a lot of my knowledge of hops is based off of this one article.)
http://www.realbeer.com/hops/aroma.html

Cheers for the great info Paulsteele, those links are quite interesting, looks like I'll have to have a munch on some hop pellets as I can't stand tea , my quest continues.

The simple answer is that yes, usually you get a higher amount of aroma components (levels of each can usually be found on the hop spec sheet) when there is a higher AA. But this can not be translated between varieties. In other words a 3% AA Saaz hop will not necessarily have less aroma component than a 15% AA Green Bullet hop. But we can usually assume that a 6% AA Saaz hop will have more of the oil that contains these components than the 3% Saaz hop.

That makes me feel better, I made the brew a couple of days ago and decided to up the quantities of each hop addition to get the same IBU and hopefully very similar flavour and aroma. Cheers fellas