It really depends. There are naming conventions to the skins directories (eg. Skin_1, Skin_2, Skin_45, etc...). Once inside these skin directories, the templates should be named based on what they are for.
For a homepage template, you can name this whatever you want (generally should be an intuitive name, like HomeTemplate.ascx). Then just enter the name of this into the HomeTemplate appconfig parameter.
For the default skin for the rest of the site, this should be named template.ascx.
If you are using template switching, you can name the file whatever you'd like because you have to enter the name of the file into the entity that you are using it for.
If you are using the feature where you skin individual pages, the file can be named whatever you like because you must create specific appconfig parameters and enter the name of that file there.
All of these files should reside within the same skin_# directory that you want to use, where # will interpreted as the skin ID (eg. if the directory was called skin_45 you would enter 45 into the DefaultSkinID appconfig parameter, and you could directly invoke this skin by passing a SkinID=45 query string parameter in any of your URLs.
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