Ok, after getting the whole bandwidth problems figured out after like 3 days in, I think most of my servers were doing ok, I just didn't know it. We have 2 servers that go together with dns fail over and each one has it's own alias so we can directly test the server. The alias was failing every day on the host rewrite but the main site was working.
I had to go into CWP and create a subdomain which then created it it's own host file with the same certs and an apache rewrite worked and nothing went down.
It was working fine with us just adding the alias to the host file directly but we know what happens now with that......
I do have another server that I am still have issues with. It's has been working fine for the most part except for one domain because I had to manually edit the host file with the certs. CWP doesn't know the certs are there so when the host files get rewrote, all of them except for this one domain are working correctly. It's a cert from cloudflare that wouldn't install through cwp.