These templates are really designed around what you can do more than for customisation. I haven't used them much but here are some ideas. You should be quite familiar with SharePoint features first.
Site Admin Templates
These will be specifically bound to non-publishing sites. So you can either live with that and add the customisations you need (which you can also resave as a template) or they're not really usable.
It's worth pointing out that .stp files are just renamed .cab files so you can crack them open and see how they work. However I would use them for learning only as modifying their contents isn't supported and may end up causing you more trouble down the track.
Server Admin Templates
Here you should have a little more flexibility. The .wsp files are also renamed .cab files. However they should be using the SharePoint feature extensibility framework and therefore be more reusable and adaptable. If this is correct then you will be able to extract the features and pull them into Visual Studio one-by-one with a tool such as WSPBuilder. You will then be able to customise them as you wish.
You won't have the source code if there is any custom code used, but you should be able to analyse and extract it with Reflector. This will allow you to make the customisations you need anyway.