It seems that you're trying to replace the
Normal.mxt file with something customized, similar to this question.
Normal.mxt is what you see as "Blank Map" upon opening ArcMap, and is the default template chosen if you cancel out of the Getting Started window.
Unfortunately, creating and editing
.mxt files has been disabled since the update to version 10.x. The only real option is to save your customization to your
.mxd file and move a copy of it to the Templates folder.
When you open a template from this window, it merely pulls in its configuration to the new Untitled project, so you are free to edit and adjust without risking harm to your custom configuration.
I made a custom toolbar with some models in it and followed this process. Upon opening ArcMap and selecting the new template, I found the custom toolbar and all models in place.
It's not an ideal solution, and won't apply your configuration to existing
.mxd documents, but can at least make it simpler for any new projects you create.