Hi Ahmed,
manifest.xml is for a solution, So if you want to define a web part deploy scope , you can define in featue.xml like the following.
<?xml version="1.0" encoding="utf-8"?>
<Feature Id="71dbb87c-7d33-41a3-90a4-3e11126385ea"
Title="EventHandlerTest2012"
Description="Description for EventHandlerTest2012"
Version="12.0.0.0"
Hidden="FALSE"
Scope="Web"
DefaultResourceFile="core"
xmlns="http://schemas.microsoft.com/sharepoint/">
<ElementManifests>
<ElementManifest Location="elements.xml"/>
</ElementManifests>
</Feature>
Thanks,
Jack