There is a great book with lots of sample code to do everything you are talking about.
Inside the Microsoft® Build Engine: Using MSBuild and Team Foundation Build
Here is how you can call clean and then the build targets and also have it compile the the debug and release configurations. C:\Windows\Microsoft.NET\Framework\v4.0.30319\msbuild main.vcxproj /t:clean;build /p:Configuration=Debug;Release /p:platform=Win32
The copy task:
<ItemGroup>
<MySourceFiles Include="c:\MySourceTree\**\*.*"/>
</ItemGroup>
<Target Name="CopyFiles">
<Copy
SourceFiles="@(MySourceFiles)"
DestinationFiles="@(MySourceFiles->'c:\MyDestinationTree\%(RecursiveDir)% (Filename)%(Extension)')"
/>
This link might help you with some of your other questions.