If you create new master pages in a presentation, you have to make sure that either all of them are applied somewhere...
in the template. Just leave a few extra slides at the end of your presentation to hold the master pages you want, then delete them at the end when you're done and know you don't want them. The most precise way to apply a master page is to right-click on it in the right-hand side of the work area and choose "Apply to All Slides" or "Apply to Selected Slides."
To save a presentation as a template, choose File > Templates > Save, name the template and select a category, and click OK. Then when you start the Impress wizard, you'll see the template in the category you selected when saving.
As for making one the default master, if you apply the one you want as default to a blank slide within the template, that should work. All additional slides you create will have that master page unless you explicitly say you want something else.
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