@Jess80808 here are some representative statistics for the honors program by college:
http://admissions.tc.umn.edu/honors/review.html
You have an excellent shot of being accepted to honors for either CSE or CBS. You should follow your interests rather than worry about “prestige”, especially when you are splitting hairs between two selective colleges. Keep in mind, too, that there are other majors besides engineering at CSE (chemistry, for instance!). Perhaps instead of focusing on the college of entry (you are a highly likely admit at either college), focus instead on what disciplines you want to pursue and then discuss with someone at the U of MN how best to do that. Or take a look at the majors of both colleges and figure out which ones seem to be a better fit for you. As long as you are pursuing the BS you are going to be exposed to a pretty rigorous program of study which, IMHO, equates to “prestige” 
UMN Admissions has been holding some “Sneak Previews” of the various colleges. I just tried to get on the website but it won’t load so I couldn’t check the dates to see if CBS and CSE had any openings. If there is space available you might consider attending both just to better understand where you see yourself.
Finally, your question about where to put the additional activities if they don’t fit the little box: Yes, just stick those in the “Other Talents, Achievements or Activities” section. That’s what my daughter is doing. She couldn’t fit some stuff in the little boxes either. If you wish, you can even make a personal statement explaining your passion for your work at the end of the application.
Good luck to you!