Create project item with the attribute in the project file.

I can easily create a project with an item having the attribute <LogicalName></LogicalName> in the projectTemplate project file by using

   <EmbeddedResource Include="some.xml">
      <SubType>Designer</SubType>
      <LogicalName>LogicalName.xml</LogicalName>
    </EmbeddedResource>

However, if I am creating a project item, there is of course no projectTemplate project file. How do I create a project vsix project item, lets say in CSharp or VisualBasic, that will create the LogicalName attribute for the item? Do I need a wizard to modify the project file? If so please give direction and approach to modifying the project file. Preferably with automatic reloading of project file if possible (without prompt from user). 

Note: vstemplate file only has the following attributes for a project item

<ProjectItem
    SubType="Form/Component/CustomControl/UserControl"
    CustomTool="string"
    ItemType="string"
    ReplaceParameters="true/false"
    TargetFileName="TargetFileName.ext">
        FileName.ext
</ProjectItem>

No LogicalName

If this is not clear, I will attempt to rephrase question.