The Remi repository aims mainly to provide the latest versions of the LAMP stack whereas Atomic repository provides much more. Depending on what you're trying to achieve, you probably shouldn't have both repositories enabled.
Neither Atomic or Remi should conflict with EPEL, so EPEL should co-exist peacefully with either.
One working option, if you really want to have both Atomic and Remi repositories for some odd reason, is to keep them both disabled by default (ie. having
enabled=0 in respective repository files, found in
/etc/yum.repos.d) and only enable them when actually updating/installing something from them (use
--enablerepo= switch with yum when installing/updating something from the repo in question).
For example, to install MySQL from Remi and Openvas from Atomic, you could do:
yum --enablerepo='*remi*' install mysql
yum --enablerepo='*tomic*' install openvas
This has the downside of having to update both MySQL and Openvas manually by enabling the respective repositories when running
yum update. So it'd be best to re-think why you have both Remi and Atomic repositories enabled/available in the first place.