I thought all elements had an aux input above the glove box. I have an 07 SC, can I easily add one by the 12v jack above my glove box? Thanks!

What's wrong with the one in the console?

It is in your console. Open the console armrest door, inside against the forward wall you will see both a 12v lighter jack and another marked "AUX". The console even has a little ridge for an MP3 player cable to run out.

I'm aware of the one in the console, but I having the one above the glove box will come in handy at times.

Maybe a stereo upgrade is your easiest way out. Pioneer has a great double din unit that is very nice in the E yet still affordable and very easy to use. Prices are going down as well. I paid $220 shipped for my AVH-P3200DVD unit. It will give you your AUX input, memory card and USB on the front panel not to mention more power, better sound, and a slew of other options to make the sound come alive.
http://www.sonicelectronix.com/item_22418_Pioneer-AVH-P3200DVD.html

I've been looking at this head unit: http://www.crutchfield.com/p_158XAV70BT/Sony-XAV-70BT.html?tp=20217&nvpair=AG_Size|FFDouble%40DIN&nvpair=FFBluetooth|Built-in&tab=review#tab

Can the factory amp be upgraded easily?

Not to knock Sony, but for that price you can have a much better unit and speakers. Not sure if you would just want to upgrade the factory amp. The factory speakers wouldnt handle an aftermarket amps power. If your upgrading the head unit, do speakers as well. If your going to upgrade the amp, make it easy on yourself and do a complete new install, new wire and all.
Thats just my opinion though.