The difference between the colleges is basically their GE requirements and location on campus.
You can use this link to compare colleges: http://provost.ucsd.edu/colleges/compare.html
There is no way to know until you are accepted if you get into your 1st choice, last choice or any choice in-between so just rank them based on what you think would work best for you. If you have a lot of AP credit, look for a college that the AP credit may help fulfill some of your GE requirements.