If you put your custom template in the same folder as the out-of the box one it will be available from the drop down menu when you open AC.
I wouldn't get rid of the AC template as it allows you to do a new and reset. This is necessary when you work with IFC files and open an IFC file without first opening the AC template you get incomplete file(s).
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"