All I am trying to do is get my dvd collection ripped so when I do get an Apple TV they will be formatted to watch on my 42 inch plasma.
All I am doing is selecting Apple Tv in the preset under handbrake as it gives me the highest bit rate. What else should I be doing? I get wrapped around the axle when the talk moves towards anamorphic etc.
Is there anything else I should know????
You don't have to understand what "anamorphic" means, just turn it on

(Try first with a short segment whether it works or not, just in case). You get smaller files at same quality or higher quality at same file size that way.
The next important thing is "de-interlacing". If your DVDs come from a TV show, turn it on. If you have movies on DVD, turn it off. If you are not sure: Look at the ten preview images that handbrake shows you. Check if you have jagged edges in scenes with motion. If that is the case, turn de-interlacing on; the second quality is fine. If you don't have it, turn de-interlacing off. You have to check this one; setting it the wrong way will reduce quality.
You get the best quality by using h.264, two pass. That also takes longest. Remember, your Mac doesn't get tired. Doesn't hurt it at all to encode movies for two weeks in a row.
Then before you start, I recommend you experiment a bit to see what quality you are happy with with short scenes instead of complete movies. Better spending an hour or two trying out things then compressing 50 DVDs and being unhappy with the results afterwards.
Next thing before you get going: Get Mac The Ripper. This one is real important when you do a whole DVD collection. Mac The Ripper just sucks the DVD onto your hard drive, so you can get quite a few DVDs on your Mac in an evening. Once that is done, you can start Handbrake and tell it to convert all those DVDs, one after the other. That can take a long time, but you won't have to swap DVDs anymore, so it can run overnight or while you're at work.