by the time you get scripting to do it properly (if you can at all) then you most likely could have just exported each one individually and batched processed them in compressor
Use the 640×480, many people will also watch iPod Videos ether on the computer or they hook up the iPod to a TV to watch. 640×480 will book much better on a computer or TV then 320×240 will. Also with the upcoming Apple TV many more people will be sending content from iTunes to the TV.
Some of it depends on where you live, but I say you definitely should be paid more. (Always pursue what you feel you are forth) Here are a few web sites that to help you out.