Since you aren’t getting any responses to this, I’ll give you my take. My daughter will be attending Baylor next year, so this is based on our perception of how things work. She applied for and was accepted into all four programs within the Honors College. She will be a University Scholars major and participating in the Honors Program. I am assuming you are specifically asking about the Honors Program and not the other options in the Honors College (BIC, University Scholars or Great Texts), so I will frame this response based on that assumption.
In the Honors Program a student takes two honors designated classes per semester for the first two years at Baylor. One class per semester is specifically required (First Year Seminar, Honors Great Text Course) and the other is chosen by the student. Some courses have an honors designation for students to select, or a student can work with a professor of a non Honors designated course for some extra work (i.e. extra paper) for an Honors designation.
The second two years focuses on the writing of an Honors thesis that is defended in front of a panel of professors. There are course hours dedicated for researching the paper, etc.
To ask your specific questions…
No the students aren’t generally separated from the other students. As a participant in one of the Honors College programs, you do have the option to apply to live in the Honors Residential College, but that is optional. It still isn’t separating you from the other students, but you would be living in a dorm with only other Honors College participants. There are also some invitation only events during your time at Baylor that are specific for Honors program participants.
At Invitation to Excellence this winter, the University Scholars head was asked whether the Honors designated courses are different than other courses and he answered that it depends on the course and the professor. The ones that are only available to Honors participants obviously are, such as the First Year Seminar. He said that he taught an intro to Latin course with an Honors designation and said it was basically the same as the non Honors designated intro to Latin course. He said other professors do however add extra work, primarily extra writing assignments for their Honors courses.
The primary tangible difference post graduation is likely the fact that you have written a Senior Thesis as an Honors program participant. This can be a great advantage if you intend to apply to graduate school and they ask for a writing sample. It also likely prepares you for transitioning into graduate school. If you don’t intend to go to graduate school, the primary benefit is that you pushed yourself in your academic pursuits in college.
This website does a good job explaining the Honors Program. Check out all the options down the left side of the page.
http://www.baylor.edu/honors_program/index.php?id=26081