I believe I started with the same thing with my 30D. I put the flash on the bracket on whichever slave mode worked best. Yes the flash will pop-up. The slave flash will go off when it sees the camera flash fire. I found it gave me more light having both, than just having the one on the shoe on top of the camera. The different slave settings were for how fast the slave fired after seeing the main flash I believe. Slave 4 seemed way slower than Slave 1. Maybe it was just me.....
I now have a professional backet and a 580 EX 2 speedlight. Having a flash on a bracket I was told cuts down on redeye and the shadows cast by an object.
Hopefully this helps a little!
I'd rather be shooting in Hawaii!