Hey Scott,
You can include the ASMX file by including a element in the <files>
section:
<files>
<file>
<name>YourWebService.asmx</name>
<path></path>
</file>
</files>
Generally, you don't need to specify a path.
Alternatively, you can include a Resources.zip file with your package which will include any files other than those that DNN needs to process during installation (e.g. Assemblies and SqlDataProvider files).
The benefit of this is maintainability. Using Resources.zip will keep you from having to edit the manifest file over and over...
The contents of the zip file will simply be unpacked into the root module directory (e.g. /DesktopModules/YourModule/*). If there is a file structure within your zip file it will be maintained.
You'll want to add TheNameOfYourFile.zip To your manifest file under the element.
[snip]
<folder>
<name>Your Module</name>
<friendlyname>Your Module</friendlyname>
<foldername>YourModule</foldername>
<modulename>YourModule</modulename>
<description>A module for DotNetNuke websites.</description>
<version>01.00.00</version>
<resourcefile>Resources.zip</resourcefile>
<businesscontrollerclass></businesscontrollerclass>
<modules>
<module>
[/snip]
As for referencing it in your module - I suggest using:
<%=ResolveUrl("~/DesktopModules/YourModule/Services.asmx")%>