Even if you take your prerequisites at an online school, you're still transferring the credits. So it's no different than going to a community college. You need to check your school's policy for allowing you to take credits at other schools. If you've been accepted they may not want you to just start taking classes at another school right away if you want to enroll with them. So you may have to just pony up the tuition and take them there, or take the classes somewhere else, which again I'll stress-you should do at a community college. You may only have those choices. If you're worried you won't get in if you don't accept now, don't be. It's hard to get into some of these colleges with a 3.5 out of high school, but many of them accept many students with a 3.0-3.5 from a community college. I got accepted as a transfer to Pitt with a 3.8, but I've known people who got in with a 3.2 and 3.1. So if you do well they probably won't think less of you if you go to a CC.
Unless we're talking MIT here, but you never said what school you were going to, so I'm assuming state-level school.
Bottom line, you need to talk to someone in admissions at your school to see what the deal is with taking classes at other schools while simultaneously being in your first semester at the school, because like I said, you may not have a choice of doing both.