I added two new websites one is working great, the other one has a messed up layout, it started with internal pages, but now even the home page looks really bad
May I ask you to post and share your domain name in bracketed dot [.] notation here with us so we could double-check, troubleshoot and provide some feedback information? 
Before moving to Cloudflare, was your Website working over HTTPS connection?
May I ask what SSL option have you got selected under the SSL/TLS tab at Cloudflare dashboard for your domain ( Flexible, Full, Full Strict … )?
Other thing which I could try to consider is the “Rocket Loader” being enabled, and/or “Auto Minify (HTML, CSS, JS)” which could somehow have an impact or be in conflict, if so