This is the sample Manifest.xml file for deploying a Application Page (layouts page) through the solution file. It is assumed that you know how to create a WSP file.
<Solution SolutionId="540C3653-5A01-4a00-A0FA-2D2203BB3080" xmlns="http://schemas.microsoft.com/sharepoint/">
<FeatureManifests>
<FeatureManifest Location="FeatureNameFeature.xml"/>
</FeatureManifests>
<Assemblies>
<Assembly DeploymentTarget ="GlobalAssemblyCache" Location ="Sample.AssemblyName.dll">
<SafeControls>
<SafeControl Assembly="AssemblyName, Version=1.0.0.0, Culture=neutral, PublicKeyToken=b51c7c45d52dacb6" Namespace="NameSpace" TypeName="*" Safe ="True"/>
</SafeControls>
</Assembly>
</Assemblies>
<TemplateFiles>
<TemplateFile Location ="LAYOUTSSample.aspx"/>
</TemplateFiles>
</Solution>
The above example is for a application page with code behind. <SafeControls> entry registers the dll as safe control and puts the dll in GAC. <TemplateFiles> entry puts the aspx page in the Layouts directory. Sameway you can target the others folders in the Template directory.
Satheesh Palaniswamy