to change the color of the private message popup here:
and the to change the color where the yellow is here:
1. You don't need to edit any templates for that.
Simply go to your theme settings and edit the global.css file:
Find:
.pm_alert {
And edit it to your needs.
2. Same way, different class.
Go to your theme settings, edit global.css file:
Find:
.trow_sep {
And edit it to your needs.