manually created DNS records being overwritten with template ones

[aseques]

To have custom DNS you have to do this way:
1.- Edit /etc/ispcp/bind/parts/db_e.tpl
2.- Comment with ; the lines you want to custom (in your case the mx servers)
3.- You have to create the mx servers for EVERY domain in your system (you could use the CLI in http://www.isp-control.net/forum/thread-4255.html because i doesn't work from the panel)
4.- This should be working and permanent now ...