Welcome to the HOD Board!

We are doing RTR this year and loving it. We are doing 3 HOD guides with our different aged sons, and the placement chart has really been on target for accurately placing them. Correct placement is a big deal. So, I'd start there and see if your kiddos match up with RTR fairly well...
http://www.heartofdakota.com/placing-your-child.php
As far as doing your own math, that's totally fine. I'm not sure what LA subject areas BJU English covers - is it just grammar? If so, you should be fine there, and it would sub in for R & S English. As far as science, you CAN sub in your own, but I'm not sure you'll want to after you see the science in RTR. We love it. Here are some of the reasons why... It is totally independent. The science books are living and so much more interesting than mere textbooks. My ds does a science experiment on his own every week - it gets done every week without fail as it uses things we have on hand in our home already, and it doesn't require me. There is a science lab form he completes each week that teaches the scientific method. He does vocabulary work, copywork, written narrations, and notebookings that are all assigned to be done independently within the HOD plans. It is all linked to the Bible. Anyway, we just wouldn't be happy with anything else because it is so well-written. However, we sometimes struggled to get science experiments done prior to doing HOD's science. We didn't have the materials sometimes, or I had to help with so much of the experiment I was really doing it instead of my ds. Or, I was having to skip the parts in contrast to Creationism. Or, it was dry. HOD fixed all of those problems for us and has made science a big hit in our house. So, yes - you can easily sub in your own science - but before you do, maybe check out how it's written in HOD and consider giving it a shot.
Whatever parts of HOD you choose to use - those parts will make doing it worthwhile! Each part of the guide provides an excellent way to learn.

Have you seen the RTR Student Notebooks? They are BEAUTIFUL! Just had to gush a tad about that. I love the keepsakes we are making of this year within the Student Notebook. I'd love to help answer any other questions you may have - I think you'll find HOD to be such a neat way to go about homeschooling! I think you'll also find the ladies on this board to be one-of-a-kind. They are a great bunch of ladies - you'll fit right in!
In Christ,
Julie