Nathan,
The first part of your request is pretty simple. Just follow these steps.
Create a highlight on a page.

Right mouse click and select Properties.

When the properties pane pops open set the color to anything that you would like.

Then select the check box labeled "Save as default" and hot OK.

You can delete that highlight we just made unless you needed it. From this point forward any new highlights you make will be that default color.

This only affects your user account.
The second part of your request is not possible unless someone knows of a third party developed tool using the SDK.
Hope this helped.
John