I installed the CPanel version of ASL and the install failed with the following error below. I'm also noticing that my MySQL 5.5 database memory usage spiked up dramatically to over 400mb of usage (the databases are under 30mb total and has been optimized). Is there any way to fix this. Prior to installing the memory usage was less than 1/3 of this.

Error:
--------
file /usr/share/mysql/charsets/Index.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/README from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/armscii8.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/ascii.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/cp1250.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/cp1251.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/cp1256.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/cp1257.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/cp850.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/cp852.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/cp866.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/dec8.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/geostd8.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/greek.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/hebrew.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/hp8.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/keybcs2.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/koi8r.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/koi8u.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/latin1.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64
file /usr/share/mysql/charsets/latin2.xml from install of mysql-libs-5.1.61-1.el6_2.1.x86_64 conflicts with file from package MySQL-server-5.5.22-2.cp.1132.x86_64

Thats a packaging bug on cpanels mysql-server package. Mysql.com fixed that one a few months ago (thats who cpanel is duplicating there). Looks like they didnt include the fixes. I'd let their support know about this one

Is there a fix I can manually apply? Also does the failed install have anything to do with a massive database ram usage spike I'm having?

What that means is that nothing happened, no packages were installed because the MySQL-server package got in the way.

Is there a way I can get Atomic Secured Linux installed and bypass this error.

Yeah upgrade to the mysql from the atomic channel. It doesnt have the bug that the cpanel one does.

Plus our version of 5.5 is much newer and has all the bug fixes put out since 5.5.25.

How would I go about updating this without breaking my existing database.

Sure the mysql page is here:
https://www.atomicorp.com/wiki/index.php/Mysql